rs9301653

Positions:

• chr13-86640314-A-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 0.148 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;