rs2819130

Variant names:

• chr1-63765870-G-A
• rs2819130

Your query was ambiguous. Multiple possible variants found:

• chr1-63765870-G-A
• chr1-63765870-G-C
• chr1-63765870-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.83 in 152,010 control chromosomes in the GnomAD database, including 52,379 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.83 (52379 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.623
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.963 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.830 AC: 126017 AN: 151894 Hom.: 52332 Cov.: 29

Gnomad AFR AF: 0.790

Gnomad AMI AF: 0.871

Gnomad AMR AF: 0.848

Gnomad ASJ AF: 0.886

Gnomad EAS AF: 0.985

Gnomad SAS AF: 0.879

Gnomad FIN AF: 0.817

Gnomad MID AF: 0.845

Gnomad NFE AF: 0.832

Gnomad OTH AF: 0.841

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.830 AC: 126119 AN: 152010 Hom.: 52379 Cov.: 29 AF XY: 0.832 AC XY: 61804 AN XY: 74288

African (AFR) AF: 0.790 AC: 32749 AN: 41432

American (AMR) AF: 0.848 AC: 12945 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.886 AC: 3074 AN: 3470

East Asian (EAS) AF: 0.985 AC: 5092 AN: 5168

South Asian (SAS) AF: 0.879 AC: 4233 AN: 4814

European-Finnish (FIN) AF: 0.817 AC: 8629 AN: 10566

Middle Eastern (MID) AF: 0.832 AC: 243 AN: 292

European-Non Finnish (NFE) AF: 0.832 AC: 56583 AN: 67976

Other (OTH) AF: 0.842 AC: 1777 AN: 2110

Alfa AF: 0.836 Hom.: 227782

Bravo AF: 0.832

Asia WGS AF: 0.901 AC: 3136 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.70
DANN	Benign	0.50
PhyloP100		-0.62

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2819130; hg19: chr1-64231541; COSMIC: COSV59949256;