rs2248359

Positions:

• chr20-54174979-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 0.464 in 152,020 control chromosomes in the GnomAD database, including 17,317 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 0.46 (17317 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.637 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.464 AC: 70423 AN: 151902 Hom.: 17272 Cov.: 32

Gnomad AFR AF: 0.643

Gnomad AMI AF: 0.417

Gnomad AMR AF: 0.372

Gnomad ASJ AF: 0.568

Gnomad EAS AF: 0.372

Gnomad SAS AF: 0.414

Gnomad FIN AF: 0.355

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.397

Gnomad OTH AF: 0.476

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

GnomAD4 genome AF: 0.464 AC: 70521 AN: 152020 Hom.: 17317 Cov.: 32 AF XY: 0.460 AC XY: 34209 AN XY: 74294

Gnomad4 AFR AF: 0.643

Gnomad4 AMR AF: 0.371

Gnomad4 ASJ AF: 0.568

Gnomad4 EAS AF: 0.372

Gnomad4 SAS AF: 0.413

Gnomad4 FIN AF: 0.355

Gnomad4 NFE AF: 0.397

Gnomad4 OTH AF: 0.479

Alfa AF: 0.415 Hom.: 29182

Bravo AF: 0.471

Asia WGS AF: 0.417 AC: 1447 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.9
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2248359; hg19: chr20-52791518; COSMIC: COSV53775496;