20-23139129-C-T

Variant names:

• chr20-23139129-C-T
• rs6083017

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 0.611 in 152,114 control chromosomes in the GnomAD database, including 28,717 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 0.61 (28717 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.235

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.663 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: 0.611 AC: 92847 AN: 151996 Hom.: 28692 Cov.: 33

Gnomad AFR AF: 0.549

Gnomad AMI AF: 0.858

Gnomad AMR AF: 0.674

Gnomad ASJ AF: 0.645

Gnomad EAS AF: 0.521

Gnomad SAS AF: 0.597

Gnomad FIN AF: 0.518

Gnomad MID AF: 0.755

Gnomad NFE AF: 0.649

Gnomad OTH AF: 0.658

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

GnomAD4 genome AF: 0.611 AC: 92908 AN: 152114 Hom.: 28717 Cov.: 33 AF XY: 0.605 AC XY: 44967 AN XY: 74360

Gnomad4 AFR AF: 0.549

Gnomad4 AMR AF: 0.674

Gnomad4 ASJ AF: 0.645

Gnomad4 EAS AF: 0.521

Gnomad4 SAS AF: 0.596

Gnomad4 FIN AF: 0.518

Gnomad4 NFE AF: 0.649

Gnomad4 OTH AF: 0.657

Alfa AF: 0.650 Hom.: 42399

Bravo AF: 0.622

Asia WGS AF: 0.593 AC: 2064 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.35
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6083017; hg19: chr20-23119766;