rs1293151

Variant names:

• chr20-54335045-C-T
• rs1293151

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 0.647 in 152,038 control chromosomes in the GnomAD database, including 32,238 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 0.65 (32238 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.44
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.754 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: 0.647 AC: 98265 AN: 151920 Hom.: 32190 Cov.: 31

Gnomad AFR AF: 0.761

Gnomad AMI AF: 0.779

Gnomad AMR AF: 0.584

Gnomad ASJ AF: 0.655

Gnomad EAS AF: 0.446

Gnomad SAS AF: 0.549

Gnomad FIN AF: 0.606

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.619

Gnomad OTH AF: 0.636

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

GnomAD4 genome AF: 0.647 AC: 98371 AN: 152038 Hom.: 32238 Cov.: 31 AF XY: 0.642 AC XY: 47709 AN XY: 74298

African (AFR) AF: 0.761 AC: 31561 AN: 41484

American (AMR) AF: 0.585 AC: 8928 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.655 AC: 2273 AN: 3472

East Asian (EAS) AF: 0.445 AC: 2290 AN: 5146

South Asian (SAS) AF: 0.550 AC: 2650 AN: 4816

European-Finnish (FIN) AF: 0.606 AC: 6400 AN: 10560

Middle Eastern (MID) AF: 0.588 AC: 173 AN: 294

European-Non Finnish (NFE) AF: 0.619 AC: 42046 AN: 67972

Other (OTH) AF: 0.634 AC: 1340 AN: 2114

Alfa AF: 0.632 Hom.: 85870

Bravo AF: 0.654

Asia WGS AF: 0.560 AC: 1947 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.25
DANN	Benign	0.79
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs1293151; hg19: chr20-52951584;