20-2190984-C-T

Position:

• chr20-2190984-C-T

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 0.125 in 152,200 control chromosomes in the GnomAD database, including 1,566 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 0.13 (1566 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0610

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.167 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.125 AC: 19059 AN: 152082 Hom.: 1569 Cov.: 32

Gnomad AFR AF: 0.0292

Gnomad AMI AF: 0.285

Gnomad AMR AF: 0.114

Gnomad ASJ AF: 0.149

Gnomad EAS AF: 0.145

Gnomad SAS AF: 0.144

Gnomad FIN AF: 0.194

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.170

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.125 AC: 19042 AN: 152200 Hom.: 1566 Cov.: 32 AF XY: 0.126 AC XY: 9382 AN XY: 74424

Gnomad4 AFR AF: 0.0291

Gnomad4 AMR AF: 0.114

Gnomad4 ASJ AF: 0.149

Gnomad4 EAS AF: 0.144

Gnomad4 SAS AF: 0.143

Gnomad4 FIN AF: 0.194

Gnomad4 NFE AF: 0.170

Gnomad4 OTH AF: 0.122

Alfa AF: 0.152 Hom.: 557

Bravo AF: 0.114

Asia WGS AF: 0.134 AC: 466 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.1
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6132407; hg19: chr20-2171630;