rs2248461

Variant names:

• chr20-54175663-G-A
• rs2248461

Your query was ambiguous. Multiple possible variants found:

• chr20-54175663-G-A
• chr20-54175663-G-C
• chr20-54175663-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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;