6-137219938-C-T

Variant names:

• chr6-137219938-C-T
• rs1327474

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 0.675 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
• Publications: 56 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.899 AC: 37327 AN: 41506

American (AMR) AF: 0.680 AC: 10399 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.615 AC: 2137 AN: 3472

East Asian (EAS) AF: 0.918 AC: 4747 AN: 5172

South Asian (SAS) AF: 0.766 AC: 3699 AN: 4828

European-Finnish (FIN) AF: 0.544 AC: 5746 AN: 10566

Middle Eastern (MID) AF: 0.633 AC: 186 AN: 294

European-Non Finnish (NFE) AF: 0.536 AC: 36400 AN: 67936

Other (OTH) AF: 0.686 AC: 1449 AN: 2112

Alfa AF: 0.587 Hom.: 93550

Bravo AF: 0.691

Asia WGS AF: 0.858 AC: 2979 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.6
DANN	Benign	0.51
PhyloP100		-0.23
PromoterAI		-0.00080	Neutral

Splicing

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

Other links and lift over

dbSNP: rs1327474; hg19: chr6-137541075;