20-21994197-C-T

Variant names:

• chr20-21994197-C-T
• rs201548

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 0.469 in 152,002 control chromosomes in the GnomAD database, including 17,744 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 0.47 (17744 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0360
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.55 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: 0.470 AC: 71340 AN: 151882 Hom.: 17744 Cov.: 32

Gnomad AFR AF: 0.316

Gnomad AMI AF: 0.510

Gnomad AMR AF: 0.372

Gnomad ASJ AF: 0.528

Gnomad EAS AF: 0.494

Gnomad SAS AF: 0.493

Gnomad FIN AF: 0.624

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.554

Gnomad OTH AF: 0.460

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

GnomAD4 genome AF: 0.469 AC: 71342 AN: 152002 Hom.: 17744 Cov.: 32 AF XY: 0.472 AC XY: 35080 AN XY: 74322

African (AFR) AF: 0.316 AC: 13086 AN: 41448

American (AMR) AF: 0.372 AC: 5679 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.528 AC: 1831 AN: 3466

East Asian (EAS) AF: 0.494 AC: 2556 AN: 5170

South Asian (SAS) AF: 0.493 AC: 2368 AN: 4804

European-Finnish (FIN) AF: 0.624 AC: 6585 AN: 10556

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.554 AC: 37681 AN: 67966

Other (OTH) AF: 0.454 AC: 960 AN: 2114

Alfa AF: 0.448 Hom.: 3643

Bravo AF: 0.442

Asia WGS AF: 0.421 AC: 1467 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.0
DANN	Benign	0.25
PhyloP100		-0.036

Splicing

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

Other links and lift over

dbSNP: rs201548; hg19: chr20-21974835;