6-136979493-T-G

Variant names:

• chr6-136979493-T-G
• rs1342641

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 0.783 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	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

Gnomad4 AFR AF: 0.891

Gnomad4 AMR AF: 0.806

Gnomad4 ASJ AF: 0.763

Gnomad4 EAS AF: 0.825

Gnomad4 SAS AF: 0.729

Gnomad4 FIN AF: 0.766

Gnomad4 NFE AF: 0.717

Gnomad4 OTH AF: 0.770

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1342641; hg19: chr6-137300630;