rs9512637

Variant names:

• chr13-27346474-T-C
• rs9512637

Your query was ambiguous. Multiple possible variants found:

• chr13-27346474-T-C
• chr13-27346474-T-G

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 0.545 in 152,054 control chromosomes in the GnomAD database, including 23,735 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 (23735 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.149
• Publications: 12 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.629 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: 0.546 AC: 82917 AN: 151936 Hom.: 23732 Cov.: 33

Gnomad AFR AF: 0.397

Gnomad AMI AF: 0.625

Gnomad AMR AF: 0.569

Gnomad ASJ AF: 0.648

Gnomad EAS AF: 0.229

Gnomad SAS AF: 0.412

Gnomad FIN AF: 0.696

Gnomad MID AF: 0.659

Gnomad NFE AF: 0.634

Gnomad OTH AF: 0.562

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

GnomAD4 genome AF: 0.545 AC: 82943 AN: 152054 Hom.: 23735 Cov.: 33 AF XY: 0.547 AC XY: 40646 AN XY: 74314

African (AFR) AF: 0.397 AC: 16450 AN: 41482

American (AMR) AF: 0.569 AC: 8697 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.648 AC: 2246 AN: 3464

East Asian (EAS) AF: 0.229 AC: 1178 AN: 5146

South Asian (SAS) AF: 0.413 AC: 1990 AN: 4818

European-Finnish (FIN) AF: 0.696 AC: 7351 AN: 10568

Middle Eastern (MID) AF: 0.661 AC: 193 AN: 292

European-Non Finnish (NFE) AF: 0.634 AC: 43092 AN: 67970

Other (OTH) AF: 0.557 AC: 1176 AN: 2112

Alfa AF: 0.593 Hom.: 87729

Bravo AF: 0.531

Asia WGS AF: 0.322 AC: 1121 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	6.7
DANN	Benign	0.58
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs9512637; hg19: chr13-27920611;