rs966715

Variant names:

• chr13-68440680-G-A
• rs966715

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 0.112 in 149,272 control chromosomes in the GnomAD database, including 1,040 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 0.11 (1040 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.834

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.176 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: 0.112 AC: 16689 AN: 149188 Hom.: 1039 Cov.: 31

Gnomad AFR AF: 0.0729

Gnomad AMI AF: 0.235

Gnomad AMR AF: 0.182

Gnomad ASJ AF: 0.192

Gnomad EAS AF: 0.159

Gnomad SAS AF: 0.172

Gnomad FIN AF: 0.0776

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.110

Gnomad OTH AF: 0.131

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

GnomAD4 genome AF: 0.112 AC: 16708 AN: 149272 Hom.: 1040 Cov.: 31 AF XY: 0.114 AC XY: 8303 AN XY: 72678

Gnomad4 AFR AF: 0.0732

Gnomad4 AMR AF: 0.182

Gnomad4 ASJ AF: 0.192

Gnomad4 EAS AF: 0.159

Gnomad4 SAS AF: 0.172

Gnomad4 FIN AF: 0.0776

Gnomad4 NFE AF: 0.110

Gnomad4 OTH AF: 0.133

Alfa AF: 0.117 Hom.: 540

Bravo AF: 0.118

Asia WGS AF: 0.176 AC: 607 AN: 3440

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.75
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs966715; hg19: chr13-69014812;