rs17596081

Variant names:

• chr1-171777136-C-A
• rs17596081

Your query was ambiguous. Multiple possible variants found:

• chr1-171777136-C-A
• chr1-171777136-C-T

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 0.141 in 152,192 control chromosomes in the GnomAD database, including 1,868 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 0.14 (1868 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.618
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.194 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: 0.141 AC: 21429 AN: 152074 Hom.: 1868 Cov.: 32

Gnomad AFR AF: 0.0458

Gnomad AMI AF: 0.215

Gnomad AMR AF: 0.119

Gnomad ASJ AF: 0.168

Gnomad EAS AF: 0.161

Gnomad SAS AF: 0.0986

Gnomad FIN AF: 0.180

Gnomad MID AF: 0.115

Gnomad NFE AF: 0.197

Gnomad OTH AF: 0.142

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

GnomAD4 genome AF: 0.141 AC: 21417 AN: 152192 Hom.: 1868 Cov.: 32 AF XY: 0.139 AC XY: 10370 AN XY: 74388

African (AFR) AF: 0.0456 AC: 1896 AN: 41540

American (AMR) AF: 0.119 AC: 1812 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.168 AC: 582 AN: 3472

East Asian (EAS) AF: 0.159 AC: 825 AN: 5178

South Asian (SAS) AF: 0.0988 AC: 477 AN: 4826

European-Finnish (FIN) AF: 0.180 AC: 1909 AN: 10592

Middle Eastern (MID) AF: 0.130 AC: 38 AN: 292

European-Non Finnish (NFE) AF: 0.197 AC: 13388 AN: 67996

Other (OTH) AF: 0.139 AC: 294 AN: 2108

Alfa AF: 0.172 Hom.: 330

Bravo AF: 0.132

Asia WGS AF: 0.117 AC: 409 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	7.8
DANN	Benign	0.70
PhyloP100		-0.62

Splicing

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

Other links and lift over

dbSNP: rs17596081; hg19: chr1-171746276;