17-10953012-T-G

Variant names:

• chr17-10953012-T-G
• rs852319

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 0.268 in 152,046 control chromosomes in the GnomAD database, including 7,094 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 0.27 (7094 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.34
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.472 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: 0.268 AC: 40738 AN: 151928 Hom.: 7075 Cov.: 33

Gnomad AFR AF: 0.477

Gnomad AMI AF: 0.212

Gnomad AMR AF: 0.197

Gnomad ASJ AF: 0.130

Gnomad EAS AF: 0.460

Gnomad SAS AF: 0.130

Gnomad FIN AF: 0.303

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.157

Gnomad OTH AF: 0.215

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

GnomAD4 genome AF: 0.268 AC: 40805 AN: 152046 Hom.: 7094 Cov.: 33 AF XY: 0.274 AC XY: 20338 AN XY: 74320

African (AFR) AF: 0.477 AC: 19781 AN: 41444

American (AMR) AF: 0.197 AC: 3012 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.130 AC: 451 AN: 3464

East Asian (EAS) AF: 0.459 AC: 2370 AN: 5158

South Asian (SAS) AF: 0.128 AC: 618 AN: 4812

European-Finnish (FIN) AF: 0.303 AC: 3204 AN: 10588

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.157 AC: 10651 AN: 67992

Other (OTH) AF: 0.223 AC: 469 AN: 2104

Alfa AF: 0.227 Hom.: 616

Bravo AF: 0.273

Asia WGS AF: 0.333 AC: 1155 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.9
DANN	Benign	0.79
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs852319; hg19: chr17-10856329; COSMIC: COSV60072543;