rs2180566

Variant names:

• chr20-31431051-C-T
• rs2180566

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 0.583 in 149,546 control chromosomes in the GnomAD database, including 26,104 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 (26104 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.16
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.719 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: 0.583 AC: 87074 AN: 149438 Hom.: 26089 Cov.: 31

Gnomad AFR AF: 0.415

Gnomad AMI AF: 0.742

Gnomad AMR AF: 0.633

Gnomad ASJ AF: 0.664

Gnomad EAS AF: 0.739

Gnomad SAS AF: 0.729

Gnomad FIN AF: 0.596

Gnomad MID AF: 0.701

Gnomad NFE AF: 0.639

Gnomad OTH AF: 0.596

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

GnomAD4 genome AF: 0.583 AC: 87113 AN: 149546 Hom.: 26104 Cov.: 31 AF XY: 0.584 AC XY: 42571 AN XY: 72926

African (AFR) AF: 0.415 AC: 16588 AN: 40006

American (AMR) AF: 0.633 AC: 9489 AN: 14992

Ashkenazi Jewish (ASJ) AF: 0.664 AC: 2303 AN: 3470

East Asian (EAS) AF: 0.739 AC: 3813 AN: 5160

South Asian (SAS) AF: 0.730 AC: 3503 AN: 4798

European-Finnish (FIN) AF: 0.596 AC: 6062 AN: 10174

Middle Eastern (MID) AF: 0.685 AC: 200 AN: 292

European-Non Finnish (NFE) AF: 0.639 AC: 43244 AN: 67666

Other (OTH) AF: 0.594 AC: 1234 AN: 2076

Alfa AF: 0.620 Hom.: 49945

Bravo AF: 0.567

Asia WGS AF: 0.698 AC: 2427 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	1.2
DANN	Benign	0.28
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs2180566; hg19: chr20-30018854;