rs2819130

chr1-63765870-G-Achr1-63765870-G-Cchr1-63765870-G-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.790

Gnomad4 AMR AF: 0.848

Gnomad4 ASJ AF: 0.886

Gnomad4 EAS AF: 0.985

Gnomad4 SAS AF: 0.879

Gnomad4 FIN AF: 0.817

Gnomad4 NFE AF: 0.832

Gnomad4 OTH AF: 0.842

Alfa AF: 0.837 Hom.: 107780

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

Splicing

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

Publications

LitVar

Other links and lift over

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