6-137219938-C-T

Variant names:

• chr6-137219938-C-T
• rs1327474

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;