6-32593082-A-C

Variant names:

• chr6-32593082-A-C
• rs28366298

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 0.266 in 151,896 control chromosomes in the GnomAD database, including 5,805 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 0.27 (5805 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.910
• Publications: 50 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.328 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: 0.266 AC: 40360 AN: 151778 Hom.: 5803 Cov.: 31

Gnomad AFR AF: 0.178

Gnomad AMI AF: 0.415

Gnomad AMR AF: 0.322

Gnomad ASJ AF: 0.330

Gnomad EAS AF: 0.340

Gnomad SAS AF: 0.255

Gnomad FIN AF: 0.233

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.302

Gnomad OTH AF: 0.268

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

GnomAD4 genome AF: 0.266 AC: 40385 AN: 151896 Hom.: 5805 Cov.: 31 AF XY: 0.263 AC XY: 19548 AN XY: 74230

African (AFR) AF: 0.178 AC: 7392 AN: 41452

American (AMR) AF: 0.323 AC: 4919 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.330 AC: 1143 AN: 3466

East Asian (EAS) AF: 0.341 AC: 1761 AN: 5158

South Asian (SAS) AF: 0.255 AC: 1224 AN: 4808

European-Finnish (FIN) AF: 0.233 AC: 2461 AN: 10556

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.302 AC: 20477 AN: 67898

Other (OTH) AF: 0.266 AC: 562 AN: 2112

Alfa AF: 0.275 Hom.: 11681

Bravo AF: 0.277

Asia WGS AF: 0.249 AC: 866 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.8
DANN	Benign	0.48
PhyloP100		-0.91

Splicing

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

Other links and lift over

dbSNP: rs28366298; hg19: chr6-32560859; COSMIC: COSV63515730;