20-51054898-T-G

Variant names:

• chr20-51054898-T-G
• rs4811117

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 0.837 in 152,180 control chromosomes in the GnomAD database, including 54,068 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 0.84 (54068 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.604
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.973 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: 0.837 AC: 127277 AN: 152062 Hom.: 54045 Cov.: 32

Gnomad AFR AF: 0.677

Gnomad AMI AF: 0.807

Gnomad AMR AF: 0.894

Gnomad ASJ AF: 0.880

Gnomad EAS AF: 0.995

Gnomad SAS AF: 0.962

Gnomad FIN AF: 0.906

Gnomad MID AF: 0.835

Gnomad NFE AF: 0.888

Gnomad OTH AF: 0.833

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

GnomAD4 genome AF: 0.837 AC: 127346 AN: 152180 Hom.: 54068 Cov.: 32 AF XY: 0.840 AC XY: 62497 AN XY: 74392

African (AFR) AF: 0.676 AC: 28050 AN: 41468

American (AMR) AF: 0.894 AC: 13677 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.880 AC: 3055 AN: 3470

East Asian (EAS) AF: 0.995 AC: 5148 AN: 5172

South Asian (SAS) AF: 0.962 AC: 4647 AN: 4830

European-Finnish (FIN) AF: 0.906 AC: 9610 AN: 10608

Middle Eastern (MID) AF: 0.827 AC: 243 AN: 294

European-Non Finnish (NFE) AF: 0.888 AC: 60419 AN: 68020

Other (OTH) AF: 0.835 AC: 1761 AN: 2110

Alfa AF: 0.870 Hom.: 78692

Bravo AF: 0.828

Asia WGS AF: 0.949 AC: 3299 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	5.3
DANN	Benign	0.64
PhyloP100		0.60

Splicing

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

Other links and lift over

dbSNP: rs4811117; hg19: chr20-49671435;