20-56541681-C-T

Variant names:

• chr20-56541681-C-T
• rs6092326

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 0.469 in 151,902 control chromosomes in the GnomAD database, including 16,918 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 0.47 (16918 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.945
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.543 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.469 AC: 71260 AN: 151784 Hom.: 16902 Cov.: 32

Gnomad AFR AF: 0.437

Gnomad AMI AF: 0.450

Gnomad AMR AF: 0.418

Gnomad ASJ AF: 0.292

Gnomad EAS AF: 0.559

Gnomad SAS AF: 0.428

Gnomad FIN AF: 0.494

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.505

Gnomad OTH AF: 0.425

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

GnomAD4 genome AF: 0.469 AC: 71303 AN: 151902 Hom.: 16918 Cov.: 32 AF XY: 0.467 AC XY: 34697 AN XY: 74242

African (AFR) AF: 0.436 AC: 18084 AN: 41440

American (AMR) AF: 0.418 AC: 6380 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.292 AC: 1011 AN: 3468

East Asian (EAS) AF: 0.560 AC: 2885 AN: 5150

South Asian (SAS) AF: 0.428 AC: 2063 AN: 4820

European-Finnish (FIN) AF: 0.494 AC: 5205 AN: 10542

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.505 AC: 34275 AN: 67928

Other (OTH) AF: 0.427 AC: 895 AN: 2098

Alfa AF: 0.480 Hom.: 81745

Bravo AF: 0.462

Asia WGS AF: 0.393 AC: 1368 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	7.7
DANN	Benign	0.86
PhyloP100		0.94

Splicing

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

Other links and lift over

dbSNP: rs6092326; hg19: chr20-55116737;