rs9301653

Variant names:

• chr13-86640314-A-T
• rs9301653

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 0.148 in 151,928 control chromosomes in the GnomAD database, including 1,965 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 0.15 (1965 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.63

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.225 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: 0.148 AC: 22480 AN: 151810 Hom.: 1953 Cov.: 32

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.107

Gnomad AMR AF: 0.136

Gnomad ASJ AF: 0.0318

Gnomad EAS AF: 0.152

Gnomad SAS AF: 0.0928

Gnomad FIN AF: 0.165

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.110

Gnomad OTH AF: 0.133

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

GnomAD4 genome AF: 0.148 AC: 22521 AN: 151928 Hom.: 1965 Cov.: 32 AF XY: 0.148 AC XY: 10987 AN XY: 74286

Gnomad4 AFR AF: 0.229

Gnomad4 AMR AF: 0.136

Gnomad4 ASJ AF: 0.0318

Gnomad4 EAS AF: 0.152

Gnomad4 SAS AF: 0.0926

Gnomad4 FIN AF: 0.165

Gnomad4 NFE AF: 0.110

Gnomad4 OTH AF: 0.136

Alfa AF: 0.146 Hom.: 215

Bravo AF: 0.149

Asia WGS AF: 0.165 AC: 574 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	9.1
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9301653; hg19: chr13-87292569;