rs1293151

Variant names:

• chr20-54335045-C-T
• rs1293151

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 0.647 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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.761

Gnomad4 AMR AF: 0.585

Gnomad4 ASJ AF: 0.655

Gnomad4 EAS AF: 0.445

Gnomad4 SAS AF: 0.550

Gnomad4 FIN AF: 0.606

Gnomad4 NFE AF: 0.619

Gnomad4 OTH AF: 0.634

Alfa AF: 0.623 Hom.: 53493

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1293151; hg19: chr20-52951584;