rs3761685

Variant names:

• chr1-160114853-T-C
• rs3761685

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 0.0907 in 152,274 control chromosomes in the GnomAD database, including 765 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 0.091 (765 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.770
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.132 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: 0.0908 AC: 13810 AN: 152156 Hom.: 770 Cov.: 33

Gnomad AFR AF: 0.0214

Gnomad AMI AF: 0.132

Gnomad AMR AF: 0.0904

Gnomad ASJ AF: 0.0709

Gnomad EAS AF: 0.141

Gnomad SAS AF: 0.0868

Gnomad FIN AF: 0.122

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.125

Gnomad OTH AF: 0.0915

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

GnomAD4 genome AF: 0.0907 AC: 13804 AN: 152274 Hom.: 765 Cov.: 33 AF XY: 0.0899 AC XY: 6693 AN XY: 74428

African (AFR) AF: 0.0213 AC: 885 AN: 41572

American (AMR) AF: 0.0903 AC: 1381 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0709 AC: 246 AN: 3470

East Asian (EAS) AF: 0.140 AC: 727 AN: 5184

South Asian (SAS) AF: 0.0882 AC: 426 AN: 4832

European-Finnish (FIN) AF: 0.122 AC: 1296 AN: 10594

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.125 AC: 8492 AN: 68008

Other (OTH) AF: 0.0915 AC: 193 AN: 2110

Alfa AF: 0.112 Hom.: 1681

Bravo AF: 0.0879

Asia WGS AF: 0.123 AC: 428 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	9.8
DANN	Benign	0.58
PhyloP100		0.77

Splicing

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

Other links and lift over

dbSNP: rs3761685; hg19: chr1-160084643;