chr20-54794480-C-T

Variant names:

• chr20-54794480-C-T
• rs13037755

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 0.17 in 152,018 control chromosomes in the GnomAD database, including 2,948 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 0.17 (2948 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.199
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.251 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: 0.170 AC: 25882 AN: 151900 Hom.: 2945 Cov.: 33

Gnomad AFR AF: 0.0456

Gnomad AMI AF: 0.198

Gnomad AMR AF: 0.134

Gnomad ASJ AF: 0.160

Gnomad EAS AF: 0.00620

Gnomad SAS AF: 0.116

Gnomad FIN AF: 0.286

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.255

Gnomad OTH AF: 0.138

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

GnomAD4 genome AF: 0.170 AC: 25885 AN: 152018 Hom.: 2948 Cov.: 33 AF XY: 0.168 AC XY: 12497 AN XY: 74310

African (AFR) AF: 0.0455 AC: 1889 AN: 41508

American (AMR) AF: 0.134 AC: 2049 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.160 AC: 554 AN: 3472

East Asian (EAS) AF: 0.00641 AC: 33 AN: 5150

South Asian (SAS) AF: 0.116 AC: 557 AN: 4822

European-Finnish (FIN) AF: 0.286 AC: 3020 AN: 10554

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.255 AC: 17298 AN: 67960

Other (OTH) AF: 0.136 AC: 287 AN: 2108

Alfa AF: 0.149 Hom.: 707

Bravo AF: 0.154

Asia WGS AF: 0.0710 AC: 248 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.6
DANN	Benign	0.63
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs13037755; hg19: chr20-53411019;