rs534232

Variant names:

• chr6-52916762-T-C
• rs534232

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 0.188 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
• Publications: 1 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 (NFE) allele frequency at 95% confidence interval = 0.26 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.0532 AC: 2213 AN: 41574

American (AMR) AF: 0.195 AC: 2984 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.333 AC: 1154 AN: 3470

East Asian (EAS) AF: 0.0840 AC: 436 AN: 5190

South Asian (SAS) AF: 0.152 AC: 735 AN: 4824

European-Finnish (FIN) AF: 0.228 AC: 2420 AN: 10594

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.263 AC: 17917 AN: 67998

Other (OTH) AF: 0.215 AC: 454 AN: 2112

Alfa AF: 0.203 Hom.: 567

Bravo AF: 0.181

Asia WGS AF: 0.0990 AC: 346 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.3
DANN	Benign	0.37
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs534232; hg19: chr6-52781560;