2-15872506-A-G

Variant names:

• chr2-15872506-A-G
• rs2380707

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 0.814 in 152,144 control chromosomes in the GnomAD database, including 50,600 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 0.81 (50600 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.815
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.873 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: 0.814 AC: 123818 AN: 152026 Hom.: 50569 Cov.: 31

Gnomad AFR AF: 0.751

Gnomad AMI AF: 0.804

Gnomad AMR AF: 0.851

Gnomad ASJ AF: 0.872

Gnomad EAS AF: 0.894

Gnomad SAS AF: 0.841

Gnomad FIN AF: 0.818

Gnomad MID AF: 0.839

Gnomad NFE AF: 0.833

Gnomad OTH AF: 0.832

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

GnomAD4 genome AF: 0.814 AC: 123905 AN: 152144 Hom.: 50600 Cov.: 31 AF XY: 0.816 AC XY: 60727 AN XY: 74376

African (AFR) AF: 0.751 AC: 31143 AN: 41460

American (AMR) AF: 0.851 AC: 13020 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.872 AC: 3029 AN: 3472

East Asian (EAS) AF: 0.894 AC: 4623 AN: 5170

South Asian (SAS) AF: 0.841 AC: 4053 AN: 4822

European-Finnish (FIN) AF: 0.818 AC: 8666 AN: 10598

Middle Eastern (MID) AF: 0.840 AC: 247 AN: 294

European-Non Finnish (NFE) AF: 0.833 AC: 56640 AN: 68016

Other (OTH) AF: 0.830 AC: 1754 AN: 2112

Alfa AF: 0.828 Hom.: 127771

Bravo AF: 0.817

Asia WGS AF: 0.816 AC: 2837 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	1.3
DANN	Benign	0.55
PhyloP100		-0.81

Splicing

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

Other links and lift over

dbSNP: rs2380707; hg19: chr2-16012630;