rs6932542

Variant names:

• chr6-32412485-A-G
• rs6932542

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 0.555 in 152,098 control chromosomes in the GnomAD database, including 23,773 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 0.55 (23773 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29
• Publications: 40 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.654 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: 0.555 AC: 84337 AN: 151978 Hom.: 23758 Cov.: 32

Gnomad AFR AF: 0.601

Gnomad AMI AF: 0.670

Gnomad AMR AF: 0.564

Gnomad ASJ AF: 0.595

Gnomad EAS AF: 0.672

Gnomad SAS AF: 0.649

Gnomad FIN AF: 0.549

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.507

Gnomad OTH AF: 0.570

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

GnomAD4 genome AF: 0.555 AC: 84393 AN: 152098 Hom.: 23773 Cov.: 32 AF XY: 0.559 AC XY: 41583 AN XY: 74338

African (AFR) AF: 0.600 AC: 24886 AN: 41466

American (AMR) AF: 0.565 AC: 8635 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.595 AC: 2063 AN: 3470

East Asian (EAS) AF: 0.673 AC: 3482 AN: 5176

South Asian (SAS) AF: 0.650 AC: 3136 AN: 4826

European-Finnish (FIN) AF: 0.549 AC: 5808 AN: 10570

Middle Eastern (MID) AF: 0.486 AC: 143 AN: 294

European-Non Finnish (NFE) AF: 0.507 AC: 34434 AN: 67982

Other (OTH) AF: 0.566 AC: 1195 AN: 2112

Alfa AF: 0.527 Hom.: 51492

Bravo AF: 0.563

Asia WGS AF: 0.639 AC: 2224 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.14
DANN	Benign	0.53
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs6932542; hg19: chr6-32380262;