2-58251044-G-A

Variant names:

• chr2-58251044-G-A
• rs13411119

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 0.411 in 151,948 control chromosomes in the GnomAD database, including 16,401 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 0.41 (16401 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.407
• Publications: 14 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.751 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: 0.410 AC: 62309 AN: 151830 Hom.: 16362 Cov.: 32

Gnomad AFR AF: 0.758

Gnomad AMI AF: 0.202

Gnomad AMR AF: 0.282

Gnomad ASJ AF: 0.242

Gnomad EAS AF: 0.280

Gnomad SAS AF: 0.303

Gnomad FIN AF: 0.311

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.275

Gnomad OTH AF: 0.351

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

GnomAD4 genome AF: 0.411 AC: 62416 AN: 151948 Hom.: 16401 Cov.: 32 AF XY: 0.408 AC XY: 30326 AN XY: 74276

African (AFR) AF: 0.758 AC: 31398 AN: 41432

American (AMR) AF: 0.283 AC: 4317 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.242 AC: 838 AN: 3466

East Asian (EAS) AF: 0.280 AC: 1446 AN: 5162

South Asian (SAS) AF: 0.302 AC: 1453 AN: 4808

European-Finnish (FIN) AF: 0.311 AC: 3282 AN: 10554

Middle Eastern (MID) AF: 0.337 AC: 99 AN: 294

European-Non Finnish (NFE) AF: 0.275 AC: 18656 AN: 67940

Other (OTH) AF: 0.352 AC: 743 AN: 2110

Alfa AF: 0.315 Hom.: 28937

Bravo AF: 0.422

Asia WGS AF: 0.359 AC: 1250 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	3.2
DANN	Benign	0.49
PhyloP100		0.41

Splicing

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

Other links and lift over

dbSNP: rs13411119; hg19: chr2-58478179; COSMIC: COSV107526409;