chr6-13506640-C-T

Variant names:

• chr6-13506640-C-T
• rs2560790

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.545 AC: 22564 AN: 41404

American (AMR) AF: 0.781 AC: 11928 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.808 AC: 2799 AN: 3466

East Asian (EAS) AF: 0.792 AC: 4081 AN: 5154

South Asian (SAS) AF: 0.803 AC: 3874 AN: 4824

European-Finnish (FIN) AF: 0.865 AC: 9165 AN: 10590

Middle Eastern (MID) AF: 0.776 AC: 228 AN: 294

European-Non Finnish (NFE) AF: 0.749 AC: 50911 AN: 67992

Other (OTH) AF: 0.725 AC: 1529 AN: 2110

Alfa AF: 0.726 Hom.: 92959

Bravo AF: 0.695

Asia WGS AF: 0.734 AC: 2555 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.4
DANN	Benign	0.83
PhyloP100		0.041

Splicing

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

Other links and lift over

dbSNP: rs2560790; hg19: chr6-13506872;