17-10957302-A-C

Variant names:

• chr17-10957302-A-C
• rs2692343

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 0.471 in 152,106 control chromosomes in the GnomAD database, including 18,486 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 0.47 (18486 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.136
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.672 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.470 AC: 71508 AN: 151988 Hom.: 18455 Cov.: 33

Gnomad AFR AF: 0.679

Gnomad AMI AF: 0.378

Gnomad AMR AF: 0.482

Gnomad ASJ AF: 0.260

Gnomad EAS AF: 0.604

Gnomad SAS AF: 0.474

Gnomad FIN AF: 0.395

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.357

Gnomad OTH AF: 0.415

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

GnomAD4 genome AF: 0.471 AC: 71598 AN: 152106 Hom.: 18486 Cov.: 33 AF XY: 0.475 AC XY: 35343 AN XY: 74336

African (AFR) AF: 0.679 AC: 28168 AN: 41496

American (AMR) AF: 0.482 AC: 7368 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.260 AC: 901 AN: 3472

East Asian (EAS) AF: 0.604 AC: 3125 AN: 5172

South Asian (SAS) AF: 0.471 AC: 2270 AN: 4818

European-Finnish (FIN) AF: 0.395 AC: 4175 AN: 10562

Middle Eastern (MID) AF: 0.354 AC: 104 AN: 294

European-Non Finnish (NFE) AF: 0.357 AC: 24252 AN: 67994

Other (OTH) AF: 0.422 AC: 891 AN: 2112

Alfa AF: 0.391 Hom.: 46865

Bravo AF: 0.487

Asia WGS AF: 0.567 AC: 1974 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.6
DANN	Benign	0.63
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs2692343; hg19: chr17-10860619;