rs9510292

Variant names:

• chr13-22677598-T-A
• rs9510292

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 0.552 in 152,014 control chromosomes in the GnomAD database, including 26,410 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 0.55 (26410 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.00
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.682 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: 0.552 AC: 83845 AN: 151896 Hom.: 26405 Cov.: 32

Gnomad AFR AF: 0.226

Gnomad AMI AF: 0.756

Gnomad AMR AF: 0.682

Gnomad ASJ AF: 0.677

Gnomad EAS AF: 0.666

Gnomad SAS AF: 0.615

Gnomad FIN AF: 0.616

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.687

Gnomad OTH AF: 0.597

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

GnomAD4 genome AF: 0.552 AC: 83860 AN: 152014 Hom.: 26410 Cov.: 32 AF XY: 0.553 AC XY: 41070 AN XY: 74302

African (AFR) AF: 0.226 AC: 9361 AN: 41458

American (AMR) AF: 0.683 AC: 10427 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.677 AC: 2350 AN: 3472

East Asian (EAS) AF: 0.666 AC: 3436 AN: 5160

South Asian (SAS) AF: 0.614 AC: 2950 AN: 4804

European-Finnish (FIN) AF: 0.616 AC: 6498 AN: 10552

Middle Eastern (MID) AF: 0.658 AC: 192 AN: 292

European-Non Finnish (NFE) AF: 0.687 AC: 46695 AN: 67980

Other (OTH) AF: 0.597 AC: 1263 AN: 2116

Alfa AF: 0.605 Hom.: 3737

Bravo AF: 0.547

Asia WGS AF: 0.619 AC: 2150 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.0050
DANN	Benign	0.25
PhyloP100		-3.0

Splicing

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

Other links and lift over

dbSNP: rs9510292; hg19: chr13-23251737; COSMIC: COSV62693035;