rs1293151

chr20-54335045-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 0.647 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;