rs2180439

Variant names:

• chr20-21872462-C-T
• rs2180439

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 0.579 in 151,976 control chromosomes in the GnomAD database, including 25,621 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 0.58 (25621 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.267
• Publications: 36 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.585 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: 0.579 AC: 87993 AN: 151858 Hom.: 25613 Cov.: 33

Gnomad AFR AF: 0.592

Gnomad AMI AF: 0.552

Gnomad AMR AF: 0.497

Gnomad ASJ AF: 0.602

Gnomad EAS AF: 0.600

Gnomad SAS AF: 0.496

Gnomad FIN AF: 0.634

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.587

Gnomad OTH AF: 0.557

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

GnomAD4 genome AF: 0.579 AC: 88033 AN: 151976 Hom.: 25621 Cov.: 33 AF XY: 0.580 AC XY: 43087 AN XY: 74288

African (AFR) AF: 0.591 AC: 24511 AN: 41460

American (AMR) AF: 0.496 AC: 7574 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.602 AC: 2088 AN: 3468

East Asian (EAS) AF: 0.600 AC: 3090 AN: 5148

South Asian (SAS) AF: 0.497 AC: 2388 AN: 4808

European-Finnish (FIN) AF: 0.634 AC: 6690 AN: 10554

Middle Eastern (MID) AF: 0.483 AC: 142 AN: 294

European-Non Finnish (NFE) AF: 0.587 AC: 39888 AN: 67964

Other (OTH) AF: 0.549 AC: 1159 AN: 2110

Alfa AF: 0.583 Hom.: 104831

Bravo AF: 0.570

Asia WGS AF: 0.499 AC: 1737 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.8
DANN	Benign	0.57
PhyloP100		0.27

Splicing

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

Other links and lift over

dbSNP: rs2180439; hg19: chr20-21853100;