chr20-51054898-T-G

Variant names:

• chr20-51054898-T-G
• rs4811117

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 0.837 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.676

Gnomad4 AMR AF: 0.894

Gnomad4 ASJ AF: 0.880

Gnomad4 EAS AF: 0.995

Gnomad4 SAS AF: 0.962

Gnomad4 FIN AF: 0.906

Gnomad4 NFE AF: 0.888

Gnomad4 OTH AF: 0.835

Alfa AF: 0.872 Hom.: 58334

Bravo AF: 0.828

Asia WGS AF: 0.949 AC: 3299 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4811117; hg19: chr20-49671435;