rs2248461

chr20-54175663-G-Achr20-54175663-G-Cchr20-54175663-G-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 0.448 in 151,982 control chromosomes in the GnomAD database, including 16,347 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 0.45 (16347 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.633 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: 0.448 AC: 67976 AN: 151864 Hom.: 16301 Cov.: 32

Gnomad AFR AF: 0.639

Gnomad AMI AF: 0.369

Gnomad AMR AF: 0.349

Gnomad ASJ AF: 0.553

Gnomad EAS AF: 0.359

Gnomad SAS AF: 0.408

Gnomad FIN AF: 0.333

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.376

Gnomad OTH AF: 0.457

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

GnomAD4 genome AF: 0.448 AC: 68078 AN: 151982 Hom.: 16347 Cov.: 32 AF XY: 0.444 AC XY: 32980 AN XY: 74320

Gnomad4 AFR AF: 0.640

Gnomad4 AMR AF: 0.349

Gnomad4 ASJ AF: 0.553

Gnomad4 EAS AF: 0.359

Gnomad4 SAS AF: 0.407

Gnomad4 FIN AF: 0.333

Gnomad4 NFE AF: 0.376

Gnomad4 OTH AF: 0.460

Alfa AF: 0.390 Hom.: 19309

Bravo AF: 0.455

Asia WGS AF: 0.409 AC: 1419 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.86
Dann	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2248461; hg19: chr20-52792202;