6-32533367-C-T

Variant names:

• chr6-32533367-C-T
• rs2157337

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 0.433 in 148,302 control chromosomes in the GnomAD database, including 15,855 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 0.43 (15855 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.02
• Publications: 17 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.529 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: 0.433 AC: 64117 AN: 148190 Hom.: 15836 Cov.: 28

Gnomad AFR AF: 0.535

Gnomad AMI AF: 0.265

Gnomad AMR AF: 0.401

Gnomad ASJ AF: 0.434

Gnomad EAS AF: 0.383

Gnomad SAS AF: 0.413

Gnomad FIN AF: 0.334

Gnomad MID AF: 0.565

Gnomad NFE AF: 0.399

Gnomad OTH AF: 0.460

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

GnomAD4 genome AF: 0.433 AC: 64166 AN: 148302 Hom.: 15855 Cov.: 28 AF XY: 0.429 AC XY: 31000 AN XY: 72238

African (AFR) AF: 0.535 AC: 21387 AN: 39990

American (AMR) AF: 0.400 AC: 5897 AN: 14726

Ashkenazi Jewish (ASJ) AF: 0.434 AC: 1500 AN: 3454

East Asian (EAS) AF: 0.382 AC: 1901 AN: 4970

South Asian (SAS) AF: 0.413 AC: 1964 AN: 4752

European-Finnish (FIN) AF: 0.334 AC: 3294 AN: 9858

Middle Eastern (MID) AF: 0.570 AC: 162 AN: 284

European-Non Finnish (NFE) AF: 0.399 AC: 26876 AN: 67296

Other (OTH) AF: 0.458 AC: 944 AN: 2062

Alfa AF: 0.415 Hom.: 1876

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.74
DANN	Benign	0.56
PhyloP100		-4.0

Splicing

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

Other links and lift over

dbSNP: rs2157337; hg19: chr6-32501144;