rs13213247

chr6-80806319-A-Cchr6-80806319-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 0.0724 in 151,390 control chromosomes in the GnomAD database, including 523 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 0.072 (523 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.986

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.177 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: 0.0723 AC: 10937 AN: 151272 Hom.: 518 Cov.: 31

Gnomad AFR AF: 0.104

Gnomad AMI AF: 0.0802

Gnomad AMR AF: 0.0677

Gnomad ASJ AF: 0.0751

Gnomad EAS AF: 0.187

Gnomad SAS AF: 0.158

Gnomad FIN AF: 0.0419

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0440

Gnomad OTH AF: 0.0638

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

GnomAD4 genome AF: 0.0724 AC: 10961 AN: 151390 Hom.: 523 Cov.: 31 AF XY: 0.0749 AC XY: 5541 AN XY: 73972

Gnomad4 AFR AF: 0.104

Gnomad4 AMR AF: 0.0685

Gnomad4 ASJ AF: 0.0751

Gnomad4 EAS AF: 0.187

Gnomad4 SAS AF: 0.158

Gnomad4 FIN AF: 0.0419

Gnomad4 NFE AF: 0.0440

Gnomad4 OTH AF: 0.0651

Alfa AF: 0.0459 Hom.: 54

Bravo AF: 0.0736

Asia WGS AF: 0.164 AC: 568 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.6
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: rs13213247; hg19: chr6-81516036;