rs10917670

Variant names:

• chr1-163063052-C-T
• rs10917670

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 0.429 in 151,924 control chromosomes in the GnomAD database, including 13,986 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 0.43 (13986 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.276
• Publications: 16 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.475 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: 0.428 AC: 65037 AN: 151806 Hom.: 13967 Cov.: 31

Gnomad AFR AF: 0.458

Gnomad AMI AF: 0.399

Gnomad AMR AF: 0.405

Gnomad ASJ AF: 0.394

Gnomad EAS AF: 0.437

Gnomad SAS AF: 0.489

Gnomad FIN AF: 0.378

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.420

Gnomad OTH AF: 0.441

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

GnomAD4 genome AF: 0.429 AC: 65116 AN: 151924 Hom.: 13986 Cov.: 31 AF XY: 0.429 AC XY: 31838 AN XY: 74240

African (AFR) AF: 0.458 AC: 18978 AN: 41426

American (AMR) AF: 0.405 AC: 6183 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.394 AC: 1366 AN: 3466

East Asian (EAS) AF: 0.437 AC: 2250 AN: 5152

South Asian (SAS) AF: 0.491 AC: 2367 AN: 4816

European-Finnish (FIN) AF: 0.378 AC: 3997 AN: 10574

Middle Eastern (MID) AF: 0.466 AC: 137 AN: 294

European-Non Finnish (NFE) AF: 0.420 AC: 28544 AN: 67926

Other (OTH) AF: 0.442 AC: 932 AN: 2108

Alfa AF: 0.424 Hom.: 21783

Bravo AF: 0.429

Asia WGS AF: 0.489 AC: 1700 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.6
DANN	Benign	0.44
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs10917670; hg19: chr1-163032842;