6-13506640-C-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 0.709 in 152,026 control chromosomes in the GnomAD database, including 39,088 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 0.71 (39088 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0410

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 (SAS) allele frequency at 95% confidence interval = 0.782 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: 0.709 AC: 107715 AN: 151908 Hom.: 39077 Cov.: 31

Gnomad AFR AF: 0.545

Gnomad AMI AF: 0.758

Gnomad AMR AF: 0.780

Gnomad ASJ AF: 0.808

Gnomad EAS AF: 0.792

Gnomad SAS AF: 0.804

Gnomad FIN AF: 0.865

Gnomad MID AF: 0.791

Gnomad NFE AF: 0.749

Gnomad OTH AF: 0.727

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

GnomAD4 genome AF: 0.709 AC: 107770 AN: 152026 Hom.: 39088 Cov.: 31 AF XY: 0.718 AC XY: 53356 AN XY: 74294

Gnomad4 AFR AF: 0.545

Gnomad4 AMR AF: 0.781

Gnomad4 ASJ AF: 0.808

Gnomad4 EAS AF: 0.792

Gnomad4 SAS AF: 0.803

Gnomad4 FIN AF: 0.865

Gnomad4 NFE AF: 0.749

Gnomad4 OTH AF: 0.725

Alfa AF: 0.740 Hom.: 52042

Bravo AF: 0.695

Asia WGS AF: 0.734 AC: 2555 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	2.4
Dann	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2560790; hg19: chr6-13506872;