10-117945191-C-G

Variant names:

• chr10-117945191-C-G
• rs2185937

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 0.467 in 151,682 control chromosomes in the GnomAD database, including 17,693 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 (17693 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.562
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.599 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: 0.467 AC: 70759 AN: 151564 Hom.: 17698 Cov.: 30

Gnomad AFR AF: 0.296

Gnomad AMI AF: 0.454

Gnomad AMR AF: 0.422

Gnomad ASJ AF: 0.636

Gnomad EAS AF: 0.302

Gnomad SAS AF: 0.618

Gnomad FIN AF: 0.598

Gnomad MID AF: 0.574

Gnomad NFE AF: 0.552

Gnomad OTH AF: 0.498

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

GnomAD4 genome AF: 0.467 AC: 70776 AN: 151682 Hom.: 17693 Cov.: 30 AF XY: 0.471 AC XY: 34873 AN XY: 74102

African (AFR) AF: 0.296 AC: 12223 AN: 41334

American (AMR) AF: 0.422 AC: 6431 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.636 AC: 2208 AN: 3470

East Asian (EAS) AF: 0.302 AC: 1545 AN: 5120

South Asian (SAS) AF: 0.618 AC: 2962 AN: 4794

European-Finnish (FIN) AF: 0.598 AC: 6287 AN: 10518

Middle Eastern (MID) AF: 0.580 AC: 167 AN: 288

European-Non Finnish (NFE) AF: 0.552 AC: 37491 AN: 67896

Other (OTH) AF: 0.498 AC: 1051 AN: 2110

Alfa AF: 0.497 Hom.: 2366

Bravo AF: 0.441

Asia WGS AF: 0.457 AC: 1593 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.32
DANN	Benign	0.51
PhyloP100		-0.56

Splicing

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

Other links and lift over

dbSNP: rs2185937; hg19: chr10-119704702;