6-32913216-C-T

Variant names:

• chr6-32913216-C-T
• rs154981

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 0.524 in 151,862 control chromosomes in the GnomAD database, including 21,126 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 0.52 (21126 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.34
• Publications: 23 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.567 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.524 AC: 79478 AN: 151744 Hom.: 21101 Cov.: 30

Gnomad AFR AF: 0.573

Gnomad AMI AF: 0.534

Gnomad AMR AF: 0.472

Gnomad ASJ AF: 0.364

Gnomad EAS AF: 0.572

Gnomad SAS AF: 0.532

Gnomad FIN AF: 0.526

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.509

Gnomad OTH AF: 0.508

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

GnomAD4 genome AF: 0.524 AC: 79553 AN: 151862 Hom.: 21126 Cov.: 30 AF XY: 0.523 AC XY: 38855 AN XY: 74230

African (AFR) AF: 0.573 AC: 23712 AN: 41402

American (AMR) AF: 0.473 AC: 7210 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.364 AC: 1263 AN: 3470

East Asian (EAS) AF: 0.572 AC: 2951 AN: 5160

South Asian (SAS) AF: 0.531 AC: 2549 AN: 4800

European-Finnish (FIN) AF: 0.526 AC: 5545 AN: 10548

Middle Eastern (MID) AF: 0.582 AC: 171 AN: 294

European-Non Finnish (NFE) AF: 0.509 AC: 34595 AN: 67920

Other (OTH) AF: 0.508 AC: 1070 AN: 2108

Alfa AF: 0.519 Hom.: 12277

Bravo AF: 0.520

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.21
DANN	Benign	0.36
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs154981; hg19: chr6-32880993;