6-32703744-T-C

Position:

• chr6-32703744-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 0.295 in 151,760 control chromosomes in the GnomAD database, including 7,038 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 (7038 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.158

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.389 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.295 AC: 44704 AN: 151642 Hom.: 7022 Cov.: 30

Gnomad AFR AF: 0.294

Gnomad AMI AF: 0.400

Gnomad AMR AF: 0.397

Gnomad ASJ AF: 0.326

Gnomad EAS AF: 0.295

Gnomad SAS AF: 0.210

Gnomad FIN AF: 0.467

Gnomad MID AF: 0.204

Gnomad NFE AF: 0.249

Gnomad OTH AF: 0.291

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

GnomAD4 genome AF: 0.295 AC: 44765 AN: 151760 Hom.: 7038 Cov.: 30 AF XY: 0.305 AC XY: 22604 AN XY: 74154

Gnomad4 AFR AF: 0.294

Gnomad4 AMR AF: 0.398

Gnomad4 ASJ AF: 0.326

Gnomad4 EAS AF: 0.295

Gnomad4 SAS AF: 0.212

Gnomad4 FIN AF: 0.467

Gnomad4 NFE AF: 0.250

Gnomad4 OTH AF: 0.288

Alfa AF: 0.268 Hom.: 3020

Bravo AF: 0.295

Asia WGS AF: 0.277 AC: 968 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.9
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9275439; hg19: chr6-32671521;