1-161715801-C-T

Variant names:

• chr1-161715801-C-T
• rs10917750

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 0.634 in 151,960 control chromosomes in the GnomAD database, including 31,613 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 0.63 (31613 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.228
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.788 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.634 AC: 96328 AN: 151842 Hom.: 31592 Cov.: 31

Gnomad AFR AF: 0.474

Gnomad AMI AF: 0.514

Gnomad AMR AF: 0.577

Gnomad ASJ AF: 0.699

Gnomad EAS AF: 0.808

Gnomad SAS AF: 0.665

Gnomad FIN AF: 0.743

Gnomad MID AF: 0.665

Gnomad NFE AF: 0.710

Gnomad OTH AF: 0.646

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

GnomAD4 genome AF: 0.634 AC: 96373 AN: 151960 Hom.: 31613 Cov.: 31 AF XY: 0.636 AC XY: 47223 AN XY: 74302

African (AFR) AF: 0.474 AC: 19630 AN: 41386

American (AMR) AF: 0.577 AC: 8802 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.699 AC: 2427 AN: 3472

East Asian (EAS) AF: 0.809 AC: 4187 AN: 5178

South Asian (SAS) AF: 0.665 AC: 3191 AN: 4802

European-Finnish (FIN) AF: 0.743 AC: 7852 AN: 10574

Middle Eastern (MID) AF: 0.667 AC: 196 AN: 294

European-Non Finnish (NFE) AF: 0.710 AC: 48249 AN: 67964

Other (OTH) AF: 0.649 AC: 1370 AN: 2110

Alfa AF: 0.678 Hom.: 58963

Bravo AF: 0.613

Asia WGS AF: 0.703 AC: 2442 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.39
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs10917750; hg19: chr1-161685591;