chr6-52185695-C-T

Variant names:

• chr6-52185695-C-T
• rs8193036

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 0.714 in 151,588 control chromosomes in the GnomAD database, including 39,418 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 (39418 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.535
• Publications: 127 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 (AMR) allele frequency at 95% confidence interval = 0.756 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: 0.714 AC: 108160 AN: 151466 Hom.: 39387 Cov.: 28

Gnomad AFR AF: 0.758

Gnomad AMI AF: 0.621

Gnomad AMR AF: 0.768

Gnomad ASJ AF: 0.772

Gnomad EAS AF: 0.298

Gnomad SAS AF: 0.560

Gnomad FIN AF: 0.589

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.734

Gnomad OTH AF: 0.751

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

GnomAD4 genome AF: 0.714 AC: 108240 AN: 151588 Hom.: 39418 Cov.: 28 AF XY: 0.703 AC XY: 52059 AN XY: 74012

African (AFR) AF: 0.757 AC: 31308 AN: 41336

American (AMR) AF: 0.768 AC: 11692 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.772 AC: 2676 AN: 3466

East Asian (EAS) AF: 0.298 AC: 1523 AN: 5118

South Asian (SAS) AF: 0.560 AC: 2674 AN: 4772

European-Finnish (FIN) AF: 0.589 AC: 6161 AN: 10452

Middle Eastern (MID) AF: 0.789 AC: 232 AN: 294

European-Non Finnish (NFE) AF: 0.734 AC: 49830 AN: 67916

Other (OTH) AF: 0.753 AC: 1579 AN: 2096

Alfa AF: 0.737 Hom.: 87294

Bravo AF: 0.731

Asia WGS AF: 0.482 AC: 1679 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	1.1
DANN	Benign	0.36
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs8193036; hg19: chr6-52050493;