rs534232

Variant names:

• chr6-52916762-T-C
• rs534232

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 0.188 in 152,264 control chromosomes in the GnomAD database, including 3,497 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 0.19 (3497 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.109

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.26 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: 0.188 AC: 28667 AN: 152146 Hom.: 3494 Cov.: 32

Gnomad AFR AF: 0.0534

Gnomad AMI AF: 0.307

Gnomad AMR AF: 0.195

Gnomad ASJ AF: 0.333

Gnomad EAS AF: 0.0852

Gnomad SAS AF: 0.151

Gnomad FIN AF: 0.228

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.263

Gnomad OTH AF: 0.217

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

GnomAD4 genome AF: 0.188 AC: 28656 AN: 152264 Hom.: 3497 Cov.: 32 AF XY: 0.186 AC XY: 13834 AN XY: 74444

Gnomad4 AFR AF: 0.0532

Gnomad4 AMR AF: 0.195

Gnomad4 ASJ AF: 0.333

Gnomad4 EAS AF: 0.0840

Gnomad4 SAS AF: 0.152

Gnomad4 FIN AF: 0.228

Gnomad4 NFE AF: 0.263

Gnomad4 OTH AF: 0.215

Alfa AF: 0.208 Hom.: 566

Bravo AF: 0.181

Asia WGS AF: 0.0990 AC: 346 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	4.3
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs534232; hg19: chr6-52781560;