20-2460006-C-T

Variant names:

• chr20-2460006-C-T
• rs2143863

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 0.871 in 152,238 control chromosomes in the GnomAD database, including 57,876 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 0.87 (57876 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.31

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 (EAS) allele frequency at 95% confidence interval = 0.955 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: 0.871 AC: 132513 AN: 152120 Hom.: 57827 Cov.: 32

Gnomad AFR AF: 0.864

Gnomad AMI AF: 0.812

Gnomad AMR AF: 0.911

Gnomad ASJ AF: 0.866

Gnomad EAS AF: 0.978

Gnomad SAS AF: 0.814

Gnomad FIN AF: 0.836

Gnomad MID AF: 0.870

Gnomad NFE AF: 0.869

Gnomad OTH AF: 0.884

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

GnomAD4 genome AF: 0.871 AC: 132621 AN: 152238 Hom.: 57876 Cov.: 32 AF XY: 0.871 AC XY: 64798 AN XY: 74412

Gnomad4 AFR AF: 0.864

Gnomad4 AMR AF: 0.911

Gnomad4 ASJ AF: 0.866

Gnomad4 EAS AF: 0.977

Gnomad4 SAS AF: 0.813

Gnomad4 FIN AF: 0.836

Gnomad4 NFE AF: 0.869

Gnomad4 OTH AF: 0.884

Alfa AF: 0.868 Hom.: 75225

Bravo AF: 0.878

Asia WGS AF: 0.883 AC: 3072 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	0.083
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2143863; hg19: chr20-2440652;