6-137219938-C-T

Position:

• chr6-137219938-C-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 0.675 in 152,084 control chromosomes in the GnomAD database, including 36,672 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 0.67 (36672 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.235

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.896 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: 0.674 AC: 102489 AN: 151966 Hom.: 36607 Cov.: 32

Gnomad AFR AF: 0.899

Gnomad AMI AF: 0.578

Gnomad AMR AF: 0.680

Gnomad ASJ AF: 0.615

Gnomad EAS AF: 0.918

Gnomad SAS AF: 0.767

Gnomad FIN AF: 0.544

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.536

Gnomad OTH AF: 0.683

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

GnomAD4 genome AF: 0.675 AC: 102617 AN: 152084 Hom.: 36672 Cov.: 32 AF XY: 0.679 AC XY: 50499 AN XY: 74322

Gnomad4 AFR AF: 0.899

Gnomad4 AMR AF: 0.680

Gnomad4 ASJ AF: 0.615

Gnomad4 EAS AF: 0.918

Gnomad4 SAS AF: 0.766

Gnomad4 FIN AF: 0.544

Gnomad4 NFE AF: 0.536

Gnomad4 OTH AF: 0.686

Alfa AF: 0.575 Hom.: 37942

Bravo AF: 0.691

Asia WGS AF: 0.858 AC: 2979 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.6
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1327474; hg19: chr6-137541075;