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SNV:1-53301978-C-T (GRCh38)

Dataset

gnomAD v4.1.0

	Exomes	Genomes	Total
Filters	No data	Pass	Not in exomes
Allele Count	-	66059	66059
Allele Number	-	151812	151812
Allele Frequency	-	0.4351	0.4351
Grpmax Filtering AF (95% confidence)	-	0.6625 East Asian	0.6625 East Asian
Number of homozygotes	-	14849	14849

External Resources

Feedback

Report an issue with this variant

Genetic Ancestry Group Frequencies

Note Local ancestry data is available for this variant by selecting the tab below. See our blog post on local ancestry inference for Admixed American samples in gnomAD for more information.

gnomAD
HGDP
1KG
Local Ancestry


	3509	5150	1197	0.6814
	7848	15238	2050	0.5150
	19945	41394	4843	0.4818
	964	2104	213	0.4582
	1533	3464	342	0.4426
	374	906	76	0.4128
	1884	4804	385	0.3922
	4088	10540	786	0.3879
	114	294	26	0.3878
	25800	67918	4931	0.3799
XX	33664	77632	7470	0.4336
XY	32395	74180	7379	0.4367
Total	66059	151812	14849	0.4351

Include:ExomesGenomes


	80	100	32	0.8000
	21	28	9	0.7500
	272	436	85	0.6239
	106	198	29	0.5354
	156	358	31	0.4358
	101	280	21	0.3607
	92	302	16	0.3046
XX	276	584	81	0.4726
XY	552	1118	142	0.4937
Total	828	1702	223	0.4865

Warning Because of low sample sizes for HGDP populations, allele frequencies may not be representative.


	660	990	223	0.6667
	365	680	108	0.5368
	669	1286	188	0.5202
	390	1020	73	0.3824
	367	990	68	0.3707
XX	1205	2476	321	0.4867
XY	1246	2490	339	0.5004
Total	2451	4966	660	0.4936


	Overall	7769	15148	0.5129
Amerindigenous	3509	4321	0.8121
African	797	1429	0.5577
European	3463	9398	0.3685
	Overall	19331	40284	0.4799
African	16209	32491	0.4989
European	3122	7793	0.4006
Total	27100	55432	0.4889

Related Variants

Liftover

The following GRCh37 variant lifts over to this variant:

1-53767650-C-T
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 22 transcripts in 1 gene.

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

intron
1. LRP8
  1. ENST00000306052.12
    MANE Select transcript for LRP8
    HGVSc
    c.245-12289G>A
  2. ENST00000347547.7
    HGVSc
    c.245-12289G>A
  3. ENST00000354412.7
    HGVSc
    c.245-12289G>A

In Silico Predictors

CADD: 4.87
SpliceAI: 0.00
Pangolin: 0.0100
phyloP: 1.44

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: 1-53301000-53302000

Expected	Observed	Constraint
188.9	146	Z = 3.12 o/e = 0.77

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: 6.320e+7 (genome samples)

Site quality approximation for all variants with 0.2 <= AF < 0.5.

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

Metric	Genome samples
SiteQuality	6.320e+7
inbreeding_coeff	0.026
AS_FS	0
AS_MQ	59.989
AS_MQRankSum	0
AS_pab_max	1
AS_QUALapprox	6.320e+7
AS_QD	19.305
AS_ReadPosRankSum	0.358
AS_SOR	0.7
AS_VarDP	6.5151
AS_VQSLOD	20.158

Read Data

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