9-1162447-T-A

Variant names:

• chr9-1162447-T-A
• rs10511428

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 0.51 in 151,984 control chromosomes in the GnomAD database, including 20,445 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 0.51 (20445 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.465
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.736 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.510 AC: 77500 AN: 151866 Hom.: 20413 Cov.: 33

Gnomad AFR AF: 0.564

Gnomad AMI AF: 0.395

Gnomad AMR AF: 0.549

Gnomad ASJ AF: 0.380

Gnomad EAS AF: 0.756

Gnomad SAS AF: 0.580

Gnomad FIN AF: 0.614

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.438

Gnomad OTH AF: 0.496

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

GnomAD4 genome AF: 0.510 AC: 77585 AN: 151984 Hom.: 20445 Cov.: 33 AF XY: 0.520 AC XY: 38634 AN XY: 74294

African (AFR) AF: 0.564 AC: 23383 AN: 41468

American (AMR) AF: 0.550 AC: 8382 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.380 AC: 1316 AN: 3464

East Asian (EAS) AF: 0.756 AC: 3902 AN: 5160

South Asian (SAS) AF: 0.580 AC: 2795 AN: 4820

European-Finnish (FIN) AF: 0.614 AC: 6488 AN: 10568

Middle Eastern (MID) AF: 0.412 AC: 121 AN: 294

European-Non Finnish (NFE) AF: 0.438 AC: 29782 AN: 67938

Other (OTH) AF: 0.501 AC: 1056 AN: 2108

Alfa AF: 0.477 Hom.: 2164

Bravo AF: 0.508

Asia WGS AF: 0.691 AC: 2402 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	9.7
DANN	Benign	0.75
PhyloP100		0.47

Splicing

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

Other links and lift over

dbSNP: rs10511428; hg19: chr9-1162447; COSMIC: COSV70075721;