6-41187288-G-C

Variant names:

• chr6-41187288-G-C
• rs2093395

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 0.29 in 152,076 control chromosomes in the GnomAD database, including 6,528 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 0.29 (6528 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.336
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.351 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: 0.290 AC: 43995 AN: 151958 Hom.: 6525 Cov.: 32

Gnomad AFR AF: 0.226

Gnomad AMI AF: 0.295

Gnomad AMR AF: 0.359

Gnomad ASJ AF: 0.301

Gnomad EAS AF: 0.345

Gnomad SAS AF: 0.337

Gnomad FIN AF: 0.311

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.301

Gnomad OTH AF: 0.292

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

GnomAD4 genome AF: 0.290 AC: 44036 AN: 152076 Hom.: 6528 Cov.: 32 AF XY: 0.293 AC XY: 21804 AN XY: 74332

African (AFR) AF: 0.226 AC: 9391 AN: 41490

American (AMR) AF: 0.359 AC: 5484 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.301 AC: 1043 AN: 3468

East Asian (EAS) AF: 0.344 AC: 1781 AN: 5170

South Asian (SAS) AF: 0.338 AC: 1630 AN: 4818

European-Finnish (FIN) AF: 0.311 AC: 3292 AN: 10578

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.301 AC: 20458 AN: 67960

Other (OTH) AF: 0.289 AC: 612 AN: 2114

Alfa AF: 0.309 Hom.: 922

Bravo AF: 0.290

Asia WGS AF: 0.367 AC: 1273 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.0
DANN	Benign	0.55
PhyloP100		0.34

Splicing

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

Other links and lift over

dbSNP: rs2093395; hg19: chr6-41155026;