rs964293

Variant names:

• chr20-54200178-C-A
• rs964293

Your query was ambiguous. Multiple possible variants found:

• chr20-54200178-C-A
• chr20-54200178-C-G
• chr20-54200178-C-T

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 0.433 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
• Publications: 13 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.556 AC: 23012 AN: 41380

American (AMR) AF: 0.417 AC: 6368 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.455 AC: 1580 AN: 3470

East Asian (EAS) AF: 0.648 AC: 3350 AN: 5166

South Asian (SAS) AF: 0.405 AC: 1948 AN: 4812

European-Finnish (FIN) AF: 0.314 AC: 3292 AN: 10480

Middle Eastern (MID) AF: 0.442 AC: 130 AN: 294

European-Non Finnish (NFE) AF: 0.365 AC: 24826 AN: 67950

Other (OTH) AF: 0.449 AC: 950 AN: 2116

Alfa AF: 0.394 Hom.: 53999

Bravo AF: 0.447

Asia WGS AF: 0.512 AC: 1776 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.47
DANN	Benign	0.51
PhyloP100		-0.095

Splicing

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

Other links and lift over

dbSNP: rs964293; hg19: chr20-52816717;