rs2145078

Variant names:

• chr20-31430739-G-A
• rs2145078

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 0.296 in 152,134 control chromosomes in the GnomAD database, including 8,299 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 0.30 (8299 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.688 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: 0.297 AC: 45093 AN: 152016 Hom.: 8292 Cov.: 33

Gnomad AFR AF: 0.0966

Gnomad AMI AF: 0.491

Gnomad AMR AF: 0.405

Gnomad ASJ AF: 0.272

Gnomad EAS AF: 0.707

Gnomad SAS AF: 0.504

Gnomad FIN AF: 0.352

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.338

Gnomad OTH AF: 0.288

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

GnomAD4 genome AF: 0.296 AC: 45104 AN: 152134 Hom.: 8299 Cov.: 33 AF XY: 0.304 AC XY: 22569 AN XY: 74354

African (AFR) AF: 0.0963 AC: 3999 AN: 41506

American (AMR) AF: 0.406 AC: 6198 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.272 AC: 943 AN: 3466

East Asian (EAS) AF: 0.707 AC: 3666 AN: 5184

South Asian (SAS) AF: 0.505 AC: 2438 AN: 4826

European-Finnish (FIN) AF: 0.352 AC: 3722 AN: 10578

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.338 AC: 23008 AN: 67978

Other (OTH) AF: 0.289 AC: 610 AN: 2110

Alfa AF: 0.326 Hom.: 14771

Bravo AF: 0.292

Asia WGS AF: 0.561 AC: 1948 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	1.6
DANN	Benign	0.62
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs2145078; hg19: chr20-30018542;