rs10511428

Variant names:

• chr9-1162447-T-A
• rs10511428

Your query was ambiguous. Multiple possible variants found:

• chr9-1162447-T-A
• chr9-1162447-T-C
• chr9-1162447-T-G

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	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

Gnomad4 AFR AF: 0.564

Gnomad4 AMR AF: 0.550

Gnomad4 ASJ AF: 0.380

Gnomad4 EAS AF: 0.756

Gnomad4 SAS AF: 0.580

Gnomad4 FIN AF: 0.614

Gnomad4 NFE AF: 0.438

Gnomad4 OTH AF: 0.501

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

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