rs3762316

Variant names:

• chr1-67306340-A-G
• rs3762316

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 0.187 in 152,048 control chromosomes in the GnomAD database, including 3,069 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 0.19 (3069 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0680
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.296 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: 0.187 AC: 28472 AN: 151930 Hom.: 3067 Cov.: 31

Gnomad AFR AF: 0.301

Gnomad AMI AF: 0.162

Gnomad AMR AF: 0.192

Gnomad ASJ AF: 0.0922

Gnomad EAS AF: 0.162

Gnomad SAS AF: 0.161

Gnomad FIN AF: 0.140

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.134

Gnomad OTH AF: 0.192

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

GnomAD4 genome AF: 0.187 AC: 28481 AN: 152048 Hom.: 3069 Cov.: 31 AF XY: 0.188 AC XY: 13965 AN XY: 74336

African (AFR) AF: 0.301 AC: 12441 AN: 41390

American (AMR) AF: 0.192 AC: 2934 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0922 AC: 320 AN: 3472

East Asian (EAS) AF: 0.162 AC: 840 AN: 5178

South Asian (SAS) AF: 0.160 AC: 771 AN: 4828

European-Finnish (FIN) AF: 0.140 AC: 1487 AN: 10586

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.134 AC: 9086 AN: 68000

Other (OTH) AF: 0.192 AC: 405 AN: 2112

Alfa AF: 0.152 Hom.: 1122

Bravo AF: 0.196

Asia WGS AF: 0.193 AC: 670 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.3
DANN	Benign	0.53
PhyloP100		0.068

Splicing

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

Other links and lift over

dbSNP: rs3762316; hg19: chr1-67772023; COSMIC: COSV52027644;