rs9512630

Variant names:

• chr13-27344502-A-C
• rs9512630

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 0.0859 in 152,226 control chromosomes in the GnomAD database, including 809 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 0.086 (809 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0250
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.121 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: 0.0860 AC: 13084 AN: 152108 Hom.: 808 Cov.: 32

Gnomad AFR AF: 0.0178

Gnomad AMI AF: 0.0866

Gnomad AMR AF: 0.0677

Gnomad ASJ AF: 0.0807

Gnomad EAS AF: 0.000963

Gnomad SAS AF: 0.0286

Gnomad FIN AF: 0.214

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.123

Gnomad OTH AF: 0.0727

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

GnomAD4 genome AF: 0.0859 AC: 13081 AN: 152226 Hom.: 809 Cov.: 32 AF XY: 0.0884 AC XY: 6581 AN XY: 74414

African (AFR) AF: 0.0177 AC: 737 AN: 41546

American (AMR) AF: 0.0677 AC: 1035 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0807 AC: 280 AN: 3470

East Asian (EAS) AF: 0.000965 AC: 5 AN: 5180

South Asian (SAS) AF: 0.0292 AC: 141 AN: 4826

European-Finnish (FIN) AF: 0.214 AC: 2265 AN: 10568

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.123 AC: 8359 AN: 68018

Other (OTH) AF: 0.0714 AC: 151 AN: 2114

Alfa AF: 0.109 Hom.: 145

Bravo AF: 0.0709

Asia WGS AF: 0.0190 AC: 67 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	5.1
DANN	Benign	0.63
PhyloP100		0.025

Splicing

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

Other links and lift over

dbSNP: rs9512630; hg19: chr13-27918639;