rs964293

chr20-54200178-C-Achr20-54200178-C-Gchr20-54200178-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 0.433 in 151,850 control chromosomes in the GnomAD database, including 14,958 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 0.43 (14958 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0950

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.63 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: 0.433 AC: 65642 AN: 151732 Hom.: 14937 Cov.: 32

Gnomad AFR AF: 0.556

Gnomad AMI AF: 0.276

Gnomad AMR AF: 0.417

Gnomad ASJ AF: 0.455

Gnomad EAS AF: 0.647

Gnomad SAS AF: 0.407

Gnomad FIN AF: 0.314

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.365

Gnomad OTH AF: 0.448

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

GnomAD4 genome AF: 0.433 AC: 65707 AN: 151850 Hom.: 14958 Cov.: 32 AF XY: 0.432 AC XY: 32018 AN XY: 74200

Gnomad4 AFR AF: 0.556

Gnomad4 AMR AF: 0.417

Gnomad4 ASJ AF: 0.455

Gnomad4 EAS AF: 0.648

Gnomad4 SAS AF: 0.405

Gnomad4 FIN AF: 0.314

Gnomad4 NFE AF: 0.365

Gnomad4 OTH AF: 0.449

Alfa AF: 0.382 Hom.: 23348

Bravo AF: 0.447

Asia WGS AF: 0.512 AC: 1776 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.47
Dann	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs964293; hg19: chr20-52816717;