chr6-136979493-T-G

Variant names:

• chr6-136979493-T-G
• rs1342641

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 0.783 in 152,212 control chromosomes in the GnomAD database, including 47,118 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 0.78 (47118 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0690
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.883 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.783 AC: 119066 AN: 152094 Hom.: 47070 Cov.: 32

Gnomad AFR AF: 0.891

Gnomad AMI AF: 0.723

Gnomad AMR AF: 0.806

Gnomad ASJ AF: 0.763

Gnomad EAS AF: 0.825

Gnomad SAS AF: 0.731

Gnomad FIN AF: 0.766

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.717

Gnomad OTH AF: 0.769

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

GnomAD4 genome AF: 0.783 AC: 119165 AN: 152212 Hom.: 47118 Cov.: 32 AF XY: 0.786 AC XY: 58479 AN XY: 74410

African (AFR) AF: 0.891 AC: 37002 AN: 41530

American (AMR) AF: 0.806 AC: 12319 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.763 AC: 2648 AN: 3470

East Asian (EAS) AF: 0.825 AC: 4271 AN: 5180

South Asian (SAS) AF: 0.729 AC: 3513 AN: 4818

European-Finnish (FIN) AF: 0.766 AC: 8128 AN: 10606

Middle Eastern (MID) AF: 0.735 AC: 216 AN: 294

European-Non Finnish (NFE) AF: 0.717 AC: 48781 AN: 68004

Other (OTH) AF: 0.770 AC: 1628 AN: 2114

Alfa AF: 0.754 Hom.: 10772

Bravo AF: 0.791

Asia WGS AF: 0.775 AC: 2694 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.6
DANN	Benign	0.71
PhyloP100		0.069

Splicing

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

Other links and lift over

dbSNP: rs1342641; hg19: chr6-137300630;