20-2460006-C-T

Variant names:

• chr20-2460006-C-T
• rs2143863

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 0.871 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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.864 AC: 35877 AN: 41532

American (AMR) AF: 0.911 AC: 13942 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.866 AC: 3006 AN: 3472

East Asian (EAS) AF: 0.977 AC: 5070 AN: 5188

South Asian (SAS) AF: 0.813 AC: 3922 AN: 4822

European-Finnish (FIN) AF: 0.836 AC: 8853 AN: 10594

Middle Eastern (MID) AF: 0.878 AC: 258 AN: 294

European-Non Finnish (NFE) AF: 0.869 AC: 59086 AN: 68008

Other (OTH) AF: 0.884 AC: 1868 AN: 2114

Alfa AF: 0.869 Hom.: 95597

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
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs2143863; hg19: chr20-2440652;