20-202581-C-T

Variant names:

• chr20-202581-C-T
• rs6033398

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 0.353 in 152,032 control chromosomes in the GnomAD database, including 10,316 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 0.35 (10316 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.871
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.507 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: 0.353 AC: 53672 AN: 151914 Hom.: 10322 Cov.: 32

Gnomad AFR AF: 0.200

Gnomad AMI AF: 0.359

Gnomad AMR AF: 0.389

Gnomad ASJ AF: 0.371

Gnomad EAS AF: 0.525

Gnomad SAS AF: 0.478

Gnomad FIN AF: 0.452

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.401

Gnomad OTH AF: 0.321

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

GnomAD4 genome AF: 0.353 AC: 53677 AN: 152032 Hom.: 10316 Cov.: 32 AF XY: 0.359 AC XY: 26716 AN XY: 74320

African (AFR) AF: 0.200 AC: 8305 AN: 41486

American (AMR) AF: 0.389 AC: 5938 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.371 AC: 1287 AN: 3468

East Asian (EAS) AF: 0.524 AC: 2705 AN: 5164

South Asian (SAS) AF: 0.479 AC: 2302 AN: 4810

European-Finnish (FIN) AF: 0.452 AC: 4770 AN: 10542

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.401 AC: 27287 AN: 67976

Other (OTH) AF: 0.318 AC: 671 AN: 2112

Alfa AF: 0.368 Hom.: 13376

Bravo AF: 0.339

Asia WGS AF: 0.441 AC: 1532 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	6.0
DANN	Benign	0.81
PhyloP100		0.87

Splicing

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

Other links and lift over

dbSNP: rs6033398; hg19: chr20-183222;