6-32681887-T-C

Position:

• chr6-32681887-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 0.259 in 152,078 control chromosomes in the GnomAD database, including 5,391 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 0.26 (5391 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.02

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.428 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: 0.259 AC: 39358 AN: 151958 Hom.: 5397 Cov.: 32

Gnomad AFR AF: 0.263

Gnomad AMI AF: 0.312

Gnomad AMR AF: 0.241

Gnomad ASJ AF: 0.293

Gnomad EAS AF: 0.444

Gnomad SAS AF: 0.243

Gnomad FIN AF: 0.183

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.256

Gnomad OTH AF: 0.271

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

GnomAD4 genome AF: 0.259 AC: 39369 AN: 152078 Hom.: 5391 Cov.: 32 AF XY: 0.255 AC XY: 19000 AN XY: 74376

Gnomad4 AFR AF: 0.262

Gnomad4 AMR AF: 0.241

Gnomad4 ASJ AF: 0.293

Gnomad4 EAS AF: 0.443

Gnomad4 SAS AF: 0.241

Gnomad4 FIN AF: 0.183

Gnomad4 NFE AF: 0.256

Gnomad4 OTH AF: 0.276

Alfa AF: 0.205 Hom.: 814

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.10
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: rs1694112; hg19: chr6-32649664;