6-132542225-T-C

Position:

• chr6-132542225-T-C

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 0.312 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.327

Gnomad4 AMR AF: 0.330

Gnomad4 ASJ AF: 0.290

Gnomad4 EAS AF: 0.134

Gnomad4 SAS AF: 0.236

Gnomad4 FIN AF: 0.389

Gnomad4 NFE AF: 0.309

Gnomad4 OTH AF: 0.301

Alfa AF: 0.306 Hom.: 884

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

Splicing

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

Publications

LitVar

Other links and lift over

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