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SNV:1-35563415-G-A (GRCh38)

Dataset

gnomAD v4.1.0

	Exomes	Genomes	Total
Filters	Pass	Pass
Allele Count	22	4	26
Allele Number	1461236	152220	1613456
Allele Frequency	0.00001506	0.00002628	0.00001611
Grpmax Filtering AF (95% confidence)	0.0001043 Admixed American	0.00002260 Admixed American	0.0001020 Admixed American
Number of homozygotes	0	0	0

External Resources

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Genetic Ancestry Group Frequencies

gnomAD
HGDP
1KG
Local Ancestry


	11	59996	0.0001833
	6	44868	0.0001337
	2	74924	0.00002669
	1	91078	0.00001098
	6	1179570	0.000005087
	0	29604	0.000
	0	63958	0.000
	0	6074	0.000
	0	912	0.000
	0	62472	0.000
XX	13	812318	0.00001600
XY	13	801138	0.00001623
Total	26	1613456	0.00001611

Include:ExomesGenomes

Related Variants

Other Alternate Alleles

This variant is multiallelic. Other alternate alleles are:

1-35563415-G-T

Liftover

The following GRCh37 variant lifts over to this variant:

1-36029016-G-A
View variant in gnomAD v2.1.1

Nearby Variants

View variants located within 20 bases of this variant.

Variant Effect Predictor

This variant falls on 4 transcripts in 1 gene.

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

synonymous
1. NCDN
  1. ENST00000373243.7
    MANE Select transcript for NCDN
    HGVSp
    p.Pro533Pro
    Domains
    PF05536 (Pfam)
    PTHR13109 (PANTHER)
  2. ENST00000356090.8
    HGVSp
    p.Pro533Pro
    Domains
    PF05536 (Pfam)
    PTHR13109 (PANTHER)
  3. ENST00000373253.7
    HGVSp
    p.Pro516Pro
    Domains
    PF05536 (Pfam)
    PTHR13109 (PANTHER)

In Silico Predictors

CADD: 5.25
SpliceAI: 0.00
Pangolin: 0.00
phyloP: -5.54

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

Genomic Constraint of Surrounding 1kb Region

Genomic constraint values displayed are for the region: 1-35563000-35564000

Expected	Observed	Constraint
259	153	Z = 6.58 o/e = 0.59

ClinVar

ClinVar Variation ID: 2638650
Conditions: not provided
Germline classification: Likely benign
Review status: criteria provided, single submitter (1 star)
Last evaluated: May 1, 2022

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: 2.978e+4 (exome samples), 3.520e+3 (genome samples)

Site quality approximation for all variants with 0 <= AF < 0.00005.

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

Metric	Exome samples	Genome samples
SiteQuality	2.978e+4	3.520e+3
inbreeding_coeff	-1.505e-5	-2.627e-5
AS_FS	0.595	4.967
AS_MQ	60	60
AS_MQRankSum	0	0.594
AS_pab_max	1	1
AS_QUALapprox	2.752e+4	3.520e+3
AS_QD	13.714	10.353
AS_ReadPosRankSum	-0.09	-0.103
AS_SOR	0.772	0.746
AS_VarDP	3.3025	2.5315
AS_VQSLOD	9.155	5.583

Read Data

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