rs9317514

chr13-65523958-T-Achr13-65523958-T-Cchr13-65523958-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 0.151 in 151,756 control chromosomes in the GnomAD database, including 1,788 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 (1788 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.108

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.194 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: 0.151 AC: 22873 AN: 151640 Hom.: 1788 Cov.: 32

Gnomad AFR AF: 0.198

Gnomad AMI AF: 0.232

Gnomad AMR AF: 0.121

Gnomad ASJ AF: 0.137

Gnomad EAS AF: 0.114

Gnomad SAS AF: 0.136

Gnomad FIN AF: 0.153

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.133

Gnomad OTH AF: 0.133

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

GnomAD4 genome AF: 0.151 AC: 22883 AN: 151756 Hom.: 1788 Cov.: 32 AF XY: 0.152 AC XY: 11288 AN XY: 74154

Gnomad4 AFR AF: 0.198

Gnomad4 AMR AF: 0.121

Gnomad4 ASJ AF: 0.137

Gnomad4 EAS AF: 0.115

Gnomad4 SAS AF: 0.135

Gnomad4 FIN AF: 0.153

Gnomad4 NFE AF: 0.133

Gnomad4 OTH AF: 0.131

Alfa AF: 0.0728 Hom.: 83

Bravo AF: 0.150

Asia WGS AF: 0.110 AC: 383 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	2.2
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: rs9317514; hg19: chr13-66098090;