20-202581-C-T

Variant names:

• chr20-202581-C-T
• rs6033398

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 0.353 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.353 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

Gnomad4 AFR AF: 0.200

Gnomad4 AMR AF: 0.389

Gnomad4 ASJ AF: 0.371

Gnomad4 EAS AF: 0.524

Gnomad4 SAS AF: 0.479

Gnomad4 FIN AF: 0.452

Gnomad4 NFE AF: 0.401

Gnomad4 OTH AF: 0.318

Alfa AF: 0.374 Hom.: 10469

Bravo AF: 0.339

Asia WGS AF: 0.441 AC: 1532 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6033398; hg19: chr20-183222;