chr9-25631132-T-C

Variant names:

• chr9-25631132-T-C
• rs10511762

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 0.328 in 151,898 control chromosomes in the GnomAD database, including 9,498 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 0.33 (9498 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.427 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: 0.328 AC: 49842 AN: 151780 Hom.: 9491 Cov.: 31

Gnomad AFR AF: 0.135

Gnomad AMI AF: 0.336

Gnomad AMR AF: 0.435

Gnomad ASJ AF: 0.376

Gnomad EAS AF: 0.210

Gnomad SAS AF: 0.277

Gnomad FIN AF: 0.456

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.412

Gnomad OTH AF: 0.347

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

GnomAD4 genome AF: 0.328 AC: 49872 AN: 151898 Hom.: 9498 Cov.: 31 AF XY: 0.329 AC XY: 24454 AN XY: 74246

African (AFR) AF: 0.135 AC: 5602 AN: 41492

American (AMR) AF: 0.436 AC: 6630 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.376 AC: 1302 AN: 3466

East Asian (EAS) AF: 0.211 AC: 1085 AN: 5148

South Asian (SAS) AF: 0.277 AC: 1336 AN: 4820

European-Finnish (FIN) AF: 0.456 AC: 4809 AN: 10552

Middle Eastern (MID) AF: 0.293 AC: 86 AN: 294

European-Non Finnish (NFE) AF: 0.412 AC: 27981 AN: 67886

Other (OTH) AF: 0.348 AC: 735 AN: 2114

Alfa AF: 0.384 Hom.: 22193

Bravo AF: 0.321

Asia WGS AF: 0.311 AC: 1086 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.058
DANN	Benign	0.65
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs10511762; hg19: chr9-25631130;