chr17-10957661-G-C

Variant names:

• chr17-10957661-G-C
• rs2692344

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 151,974 control chromosomes in the GnomAD database, including 18,472 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 (18472 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0630
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.673 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: 0.471 AC: 71476 AN: 151856 Hom.: 18441 Cov.: 32

Gnomad AFR AF: 0.679

Gnomad AMI AF: 0.379

Gnomad AMR AF: 0.482

Gnomad ASJ AF: 0.260

Gnomad EAS AF: 0.603

Gnomad SAS AF: 0.475

Gnomad FIN AF: 0.396

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.357

Gnomad OTH AF: 0.416

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

GnomAD4 genome AF: 0.471 AC: 71566 AN: 151974 Hom.: 18472 Cov.: 32 AF XY: 0.476 AC XY: 35338 AN XY: 74306

African (AFR) AF: 0.679 AC: 28146 AN: 41436

American (AMR) AF: 0.482 AC: 7370 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.260 AC: 901 AN: 3468

East Asian (EAS) AF: 0.604 AC: 3117 AN: 5164

South Asian (SAS) AF: 0.472 AC: 2277 AN: 4820

European-Finnish (FIN) AF: 0.396 AC: 4185 AN: 10556

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

European-Non Finnish (NFE) AF: 0.357 AC: 24231 AN: 67934

Other (OTH) AF: 0.422 AC: 891 AN: 2110

Alfa AF: 0.258 Hom.: 583

Bravo AF: 0.487

Asia WGS AF: 0.566 AC: 1971 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.76
DANN	Benign	0.34
PhyloP100		0.063

Splicing

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

Other links and lift over

dbSNP: rs2692344; hg19: chr17-10860978;