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SNV:20-63693211-C-T (GRCh38)

Dataset

gnomAD v4.1.0

	Exomes	Genomes	Total
Filters	Pass	Pass
Allele Count	81	11	92
Allele Number	1459954	152040	1611994
Allele Frequency	0.00005548	0.00007235	0.00005707
Grpmax Filtering AF (95% confidence)	0.00004901 European (non-Finnish)	0.00004746 African/African American	0.00004865 European (non-Finnish)
Number of homozygotes	0	0	0

External Resources

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Genetic Ancestry Group Frequencies

gnomAD
HGDP
1KG
Local Ancestry


	7	91090	0.00007685
	2	29578	0.00006762
	5	74836	0.00006681
	4	62426	0.00006408
	71	1179530	0.00006019
	3	59958	0.00005004
	0	44892	0.000
	0	62694	0.000
	0	6078	0.000
	0	912	0.000
XX	40	811462	0.00004929
XY	52	800532	0.00006496
Total	92	1611994	0.00005707

Include:ExomesGenomes

Related Variants

Other Alternate Alleles

This variant is multiallelic. Other alternate alleles are:

Liftover

The following GRCh37 variant lifts over to this variant:

20-62324564-C-T
View variant in gnomAD v2.1.1

Nearby Variants

View variants located within 20 bases of this variant.

Ensembl Variant Effect Predictor

This variant falls on 10 transcripts in 2 genes.

Note The gene symbols shown below are provided by VEP and may differ from the symbol shown on gene pages.

stop gained
1. RTEL1
  1. ENST00000360203.11
    MANE Select transcript for RTEL1
    HGVSp
    p.Arg974Ter
    Domains
    cd13932 (CDD)
    pLoF
    High-confidence
  2. ENST00000318100.9
    HGVSp
    p.Arg751Ter
    Domains
    cd13932 (CDD)
    pLoF
    High-confidence
  3. ENST00000370018.7
    HGVSp
    p.Arg974Ter
    Domains
    cd13932 (CDD)
    pLoF
    High-confidence
3' UTR
1. RTEL1-TNFRSF6B
  1. ENST00000492259.6
    Ensembl canonical transcript for RTEL1-TNFRSF6B
    HGVSc
    c.*522C>T
non coding transcript exon
1. RTEL1
  1. ENST00000370003.2
    HGVSc
    n.900C>T
2. RTEL1-TNFRSF6B
  1. ENST00000480273.5
    HGVSc
    n.3005C>T
  2. ENST00000496281.2
    HGVSc
    n.2931C>T

In Silico Predictors

CADD: 39.0
SpliceAI: 0.0700
Pangolin: -0.290
phyloP: 5.77

Note For more detailed and up to date SpliceAI and Pangolin predictions, please visit our SpliceAI Lookup browser

Genomic Constraint of Surrounding 1kb Region

This variant does not have non coding constraint data for the surrounding region.

ClinVar

ClinVar Variation ID: 42020
Conditions: Dyskeratosis congenita, autosomal recessive 5, Pulmonary fibrosis and/or bone marrow failure, Telomere-related, 3, not provided, Interstitial lung disease 2, Dyskeratosis congenita, Pulmonary fibrosis
Germline classification: Pathogenic
Review status: criteria provided, multiple submitters, no conflicts (2 stars)
Last evaluated: October 1, 2024

or find more information on the ClinVar website. Data displayed here is from ClinVar's February 1, 2025 release.

Age Distribution

Exome
Genome

Variant carriers
All individuals

Include heterozygous variant carriersInclude homozygous variant carriersCompare to all individuals

Sequencing types:

Genotype Quality Metrics

Genotype quality
Depth
Allele balance for heterozygotes

Exome
Genome

Variant carriers
All individuals

Compare to all individualsSequencing types:

Site Quality Metrics

Metric distribution
All metric values

Exome
Genome

Metric: Sequencing types:

Value: 1.127e+5 (exome samples), 1.451e+4 (genome samples)

Site quality approximation for all variants with 0.00005 <= AF < 0.0001.

Note: These are site-level quality metrics, they may be unpredictable for multi-allelic sites.

Metric	Exome samples	Genome samples
SiteQuality	1.127e+5	1.451e+4
inbreeding_coeff	-5.541e-5	-7.225e-5
AS_FS	1.113	2.452
AS_MQ	59.999	59.988
AS_MQRankSum	0	0.138
AS_pab_max	1	1
AS_QUALapprox	1.080e+5	1.385e+4
AS_QD	12.393	14.89
AS_ReadPosRankSum	-0.095	0.509
AS_SOR	0.794	0.658
AS_VarDP	3.9401	2.9685
AS_VQSLOD	7.551	1.318

Read Data

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