chr6-137646115-C-T

Variant names:

• chr6-137646115-C-T
• rs12527282

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 0.243 in 152,004 control chromosomes in the GnomAD database, including 4,693 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 0.24 (4693 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.262
• Publications: 16 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.283 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: 0.243 AC: 36868 AN: 151886 Hom.: 4689 Cov.: 31

Gnomad AFR AF: 0.188

Gnomad AMI AF: 0.401

Gnomad AMR AF: 0.290

Gnomad ASJ AF: 0.342

Gnomad EAS AF: 0.0960

Gnomad SAS AF: 0.256

Gnomad FIN AF: 0.224

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.271

Gnomad OTH AF: 0.246

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

GnomAD4 genome AF: 0.243 AC: 36872 AN: 152004 Hom.: 4693 Cov.: 31 AF XY: 0.241 AC XY: 17940 AN XY: 74306

African (AFR) AF: 0.188 AC: 7790 AN: 41444

American (AMR) AF: 0.291 AC: 4436 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.342 AC: 1188 AN: 3470

East Asian (EAS) AF: 0.0958 AC: 496 AN: 5178

South Asian (SAS) AF: 0.257 AC: 1234 AN: 4804

European-Finnish (FIN) AF: 0.224 AC: 2361 AN: 10562

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.271 AC: 18404 AN: 67962

Other (OTH) AF: 0.245 AC: 517 AN: 2112

Alfa AF: 0.268 Hom.: 11994

Bravo AF: 0.248

Asia WGS AF: 0.156 AC: 544 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.8
DANN	Benign	0.85
PhyloP100		0.26

Splicing

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

Other links and lift over

dbSNP: rs12527282; hg19: chr6-137967252;