2-129382368-G-A

Variant names:

• chr2-129382368-G-A
• rs1608578

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 0.139 in 151,986 control chromosomes in the GnomAD database, including 3,088 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 0.14 (3088 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.352 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.139 AC: 21110 AN: 151868 Hom.: 3072 Cov.: 33

Gnomad AFR AF: 0.357

Gnomad AMI AF: 0.0373

Gnomad AMR AF: 0.142

Gnomad ASJ AF: 0.0231

Gnomad EAS AF: 0.249

Gnomad SAS AF: 0.130

Gnomad FIN AF: 0.0436

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0208

Gnomad OTH AF: 0.119

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

GnomAD4 genome AF: 0.139 AC: 21155 AN: 151986 Hom.: 3088 Cov.: 33 AF XY: 0.139 AC XY: 10324 AN XY: 74294

African (AFR) AF: 0.357 AC: 14805 AN: 41444

American (AMR) AF: 0.142 AC: 2174 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0231 AC: 80 AN: 3466

East Asian (EAS) AF: 0.248 AC: 1285 AN: 5174

South Asian (SAS) AF: 0.128 AC: 614 AN: 4812

European-Finnish (FIN) AF: 0.0436 AC: 459 AN: 10536

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.0208 AC: 1416 AN: 67962

Other (OTH) AF: 0.124 AC: 261 AN: 2112

Alfa AF: 0.0658 Hom.: 232

Bravo AF: 0.156

Asia WGS AF: 0.218 AC: 759 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.058
DANN	Benign	0.62
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs1608578; hg19: chr2-130139941;