rs3761685

Variant names:

• chr1-160114853-T-C
• rs3761685

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 0.0907 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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.0213

Gnomad4 AMR AF: 0.0903

Gnomad4 ASJ AF: 0.0709

Gnomad4 EAS AF: 0.140

Gnomad4 SAS AF: 0.0882

Gnomad4 FIN AF: 0.122

Gnomad4 NFE AF: 0.125

Gnomad4 OTH AF: 0.0915

Alfa AF: 0.114 Hom.: 1370

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3761685; hg19: chr1-160084643;