6-153962074-C-T

Variant names:

• chr6-153962074-C-T
• rs647303

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 0.801 in 151,294 control chromosomes in the GnomAD database, including 48,849 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 0.80 (48849 hom., cov: 27)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0100
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.882 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.801 AC: 121043 AN: 151176 Hom.: 48823 Cov.: 27

Gnomad AFR AF: 0.890

Gnomad AMI AF: 0.840

Gnomad AMR AF: 0.833

Gnomad ASJ AF: 0.671

Gnomad EAS AF: 0.757

Gnomad SAS AF: 0.792

Gnomad FIN AF: 0.826

Gnomad MID AF: 0.672

Gnomad NFE AF: 0.746

Gnomad OTH AF: 0.785

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

GnomAD4 genome AF: 0.801 AC: 121117 AN: 151294 Hom.: 48849 Cov.: 27 AF XY: 0.803 AC XY: 59327 AN XY: 73854

African (AFR) AF: 0.890 AC: 36668 AN: 41210

American (AMR) AF: 0.833 AC: 12668 AN: 15200

Ashkenazi Jewish (ASJ) AF: 0.671 AC: 2326 AN: 3464

East Asian (EAS) AF: 0.757 AC: 3876 AN: 5122

South Asian (SAS) AF: 0.790 AC: 3793 AN: 4802

European-Finnish (FIN) AF: 0.826 AC: 8556 AN: 10358

Middle Eastern (MID) AF: 0.671 AC: 196 AN: 292

European-Non Finnish (NFE) AF: 0.746 AC: 50628 AN: 67830

Other (OTH) AF: 0.779 AC: 1643 AN: 2108

Alfa AF: 0.755 Hom.: 29813

Bravo AF: 0.805

Asia WGS AF: 0.756 AC: 2621 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	5.8
DANN	Benign	0.35
PhyloP100		0.010

Splicing

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

Other links and lift over

dbSNP: rs647303; hg19: chr6-154283209;