6-132542225-T-C

Variant names:

• chr6-132542225-T-C
• rs2788935

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 0.312 in 151,350 control chromosomes in the GnomAD database, including 7,540 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 0.31 (7540 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.726
• Publications: 1 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 = 0.323 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: 0.312 AC: 47210 AN: 151230 Hom.: 7539 Cov.: 32

Gnomad AFR AF: 0.328

Gnomad AMI AF: 0.265

Gnomad AMR AF: 0.330

Gnomad ASJ AF: 0.290

Gnomad EAS AF: 0.135

Gnomad SAS AF: 0.235

Gnomad FIN AF: 0.389

Gnomad MID AF: 0.217

Gnomad NFE AF: 0.309

Gnomad OTH AF: 0.304

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

GnomAD4 genome AF: 0.312 AC: 47244 AN: 151350 Hom.: 7540 Cov.: 32 AF XY: 0.311 AC XY: 23012 AN XY: 73984

African (AFR) AF: 0.327 AC: 13390 AN: 40892

American (AMR) AF: 0.330 AC: 5028 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.290 AC: 1007 AN: 3470

East Asian (EAS) AF: 0.134 AC: 696 AN: 5176

South Asian (SAS) AF: 0.236 AC: 1134 AN: 4814

European-Finnish (FIN) AF: 0.389 AC: 4109 AN: 10574

Middle Eastern (MID) AF: 0.209 AC: 61 AN: 292

European-Non Finnish (NFE) AF: 0.309 AC: 20945 AN: 67888

Other (OTH) AF: 0.301 AC: 633 AN: 2104

Alfa AF: 0.306 Hom.: 917

Bravo AF: 0.307

Asia WGS AF: 0.179 AC: 621 AN: 3452

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.35
DANN	Benign	0.52
PhyloP100		-0.73

Splicing

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

Other links and lift over

dbSNP: rs2788935; hg19: chr6-132863364; COSMIC: COSV71512312;