6-137639227-G-T

Position:

• chr6-137639227-G-T

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 0.182 in 152,200 control chromosomes in the GnomAD database, including 3,077 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 0.18 (3077 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.229

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.305 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.182 AC: 27682 AN: 152082 Hom.: 3068 Cov.: 33

Gnomad AFR AF: 0.310

Gnomad AMI AF: 0.123

Gnomad AMR AF: 0.130

Gnomad ASJ AF: 0.134

Gnomad EAS AF: 0.206

Gnomad SAS AF: 0.114

Gnomad FIN AF: 0.103

Gnomad MID AF: 0.182

Gnomad NFE AF: 0.135

Gnomad OTH AF: 0.167

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

GnomAD4 genome AF: 0.182 AC: 27715 AN: 152200 Hom.: 3077 Cov.: 33 AF XY: 0.177 AC XY: 13165 AN XY: 74426

Gnomad4 AFR AF: 0.310

Gnomad4 AMR AF: 0.130

Gnomad4 ASJ AF: 0.134

Gnomad4 EAS AF: 0.204

Gnomad4 SAS AF: 0.114

Gnomad4 FIN AF: 0.103

Gnomad4 NFE AF: 0.135

Gnomad4 OTH AF: 0.164

Alfa AF: 0.143 Hom.: 3202

Bravo AF: 0.188

Asia WGS AF: 0.166 AC: 576 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.23
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs566097; hg19: chr6-137960364; COSMIC: COSV69428217;