17-10957661-G-C

Variant names:

• chr17-10957661-G-C
• rs2692344

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 0.471 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.471 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

Gnomad4 AFR AF: 0.679

Gnomad4 AMR AF: 0.482

Gnomad4 ASJ AF: 0.260

Gnomad4 EAS AF: 0.604

Gnomad4 SAS AF: 0.472

Gnomad4 FIN AF: 0.396

Gnomad4 NFE AF: 0.357

Gnomad4 OTH AF: 0.422

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2692344; hg19: chr17-10860978;