rs1081681

Variant names:

• chr17-35328755-T-G
• rs1081681

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 0.622 in 152,042 control chromosomes in the GnomAD database, including 31,617 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 0.62 (31617 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.58
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.879 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.622 AC: 94492 AN: 151924 Hom.: 31566 Cov.: 32

Gnomad AFR AF: 0.886

Gnomad AMI AF: 0.507

Gnomad AMR AF: 0.592

Gnomad ASJ AF: 0.499

Gnomad EAS AF: 0.541

Gnomad SAS AF: 0.478

Gnomad FIN AF: 0.481

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.516

Gnomad OTH AF: 0.586

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

GnomAD4 genome AF: 0.622 AC: 94603 AN: 152042 Hom.: 31617 Cov.: 32 AF XY: 0.617 AC XY: 45862 AN XY: 74306

African (AFR) AF: 0.886 AC: 36754 AN: 41472

American (AMR) AF: 0.592 AC: 9037 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.499 AC: 1728 AN: 3466

East Asian (EAS) AF: 0.541 AC: 2798 AN: 5174

South Asian (SAS) AF: 0.478 AC: 2306 AN: 4822

European-Finnish (FIN) AF: 0.481 AC: 5069 AN: 10538

Middle Eastern (MID) AF: 0.544 AC: 160 AN: 294

European-Non Finnish (NFE) AF: 0.516 AC: 35052 AN: 67978

Other (OTH) AF: 0.586 AC: 1237 AN: 2112

Alfa AF: 0.602 Hom.: 3765

Bravo AF: 0.644

Asia WGS AF: 0.535 AC: 1862 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.50
DANN	Benign	0.39
PhyloP100		-3.6

Splicing

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

Other links and lift over

dbSNP: rs1081681; hg19: chr17-33655774; COSMIC: COSV73952688;