6-32658472-T-C

Variant names:

• chr6-32658472-T-C
• rs6928482

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 0.473 in 151,546 control chromosomes in the GnomAD database, including 17,317 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 0.47 (17317 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.97
• Publications: 42 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.578 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: 0.473 AC: 71608 AN: 151426 Hom.: 17307 Cov.: 30

Gnomad AFR AF: 0.447

Gnomad AMI AF: 0.537

Gnomad AMR AF: 0.587

Gnomad ASJ AF: 0.569

Gnomad EAS AF: 0.558

Gnomad SAS AF: 0.392

Gnomad FIN AF: 0.432

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.462

Gnomad OTH AF: 0.497

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

GnomAD4 genome AF: 0.473 AC: 71659 AN: 151546 Hom.: 17317 Cov.: 30 AF XY: 0.472 AC XY: 34984 AN XY: 74056

African (AFR) AF: 0.447 AC: 18468 AN: 41306

American (AMR) AF: 0.588 AC: 8959 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.569 AC: 1969 AN: 3458

East Asian (EAS) AF: 0.559 AC: 2875 AN: 5140

South Asian (SAS) AF: 0.390 AC: 1875 AN: 4808

European-Finnish (FIN) AF: 0.432 AC: 4545 AN: 10530

Middle Eastern (MID) AF: 0.582 AC: 171 AN: 294

European-Non Finnish (NFE) AF: 0.462 AC: 31274 AN: 67760

Other (OTH) AF: 0.493 AC: 1035 AN: 2098

Alfa AF: 0.479 Hom.: 30191

Bravo AF: 0.493

Asia WGS AF: 0.433 AC: 1507 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.24
DANN	Benign	0.71
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs6928482; hg19: chr6-32626249;