rs9512637

chr13-27346474-T-Cchr13-27346474-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 0.545 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.397

Gnomad4 AMR AF: 0.569

Gnomad4 ASJ AF: 0.648

Gnomad4 EAS AF: 0.229

Gnomad4 SAS AF: 0.413

Gnomad4 FIN AF: 0.696

Gnomad4 NFE AF: 0.634

Gnomad4 OTH AF: 0.557

Alfa AF: 0.611 Hom.: 61324

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9512637; hg19: chr13-27920611;