rs9634463

chr13-107118887-C-T

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 0.268 in 151,992 control chromosomes in the GnomAD database, including 5,705 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 0.27 (5705 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.756

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.386 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: 0.268 AC: 40725 AN: 151872 Hom.: 5709 Cov.: 32

Gnomad AFR AF: 0.329

Gnomad AMI AF: 0.0976

Gnomad AMR AF: 0.204

Gnomad ASJ AF: 0.256

Gnomad EAS AF: 0.402

Gnomad SAS AF: 0.330

Gnomad FIN AF: 0.301

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.230

Gnomad OTH AF: 0.234

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

GnomAD4 genome AF: 0.268 AC: 40742 AN: 151992 Hom.: 5705 Cov.: 32 AF XY: 0.271 AC XY: 20167 AN XY: 74308

Gnomad4 AFR AF: 0.329

Gnomad4 AMR AF: 0.205

Gnomad4 ASJ AF: 0.256

Gnomad4 EAS AF: 0.401

Gnomad4 SAS AF: 0.330

Gnomad4 FIN AF: 0.301

Gnomad4 NFE AF: 0.230

Gnomad4 OTH AF: 0.236

Alfa AF: 0.253 Hom.: 624

Bravo AF: 0.261

Asia WGS AF: 0.366 AC: 1271 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
Cadd	Benign	7.1
Dann	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9634463; hg19: chr13-107771235;