rs3762315

Variant names:

• chr1-67306328-A-G
• rs3762315

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 152,046 control chromosomes in the GnomAD database, including 3,072 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 (3072 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.651
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• 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: 28474 AN: 151928 Hom.: 3070 Cov.: 32

Gnomad AFR AF: 0.301

Gnomad AMI AF: 0.162

Gnomad AMR AF: 0.192

Gnomad ASJ AF: 0.0922

Gnomad EAS AF: 0.163

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: 28483 AN: 152046 Hom.: 3072 Cov.: 32 AF XY: 0.188 AC XY: 13965 AN XY: 74336

African (AFR) AF: 0.300 AC: 12444 AN: 41416

American (AMR) AF: 0.192 AC: 2933 AN: 15272

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

East Asian (EAS) AF: 0.162 AC: 841 AN: 5178

South Asian (SAS) AF: 0.160 AC: 769 AN: 4820

European-Finnish (FIN) AF: 0.140 AC: 1483 AN: 10566

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

European-Non Finnish (NFE) AF: 0.134 AC: 9090 AN: 68002

Other (OTH) AF: 0.192 AC: 406 AN: 2114

Alfa AF: 0.158 Hom.: 1554

Bravo AF: 0.196

Asia WGS AF: 0.194 AC: 672 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.7
DANN	Benign	0.74
PhyloP100		0.65

Splicing

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

Other links and lift over

dbSNP: rs3762315; hg19: chr1-67772011;