rs2115322

Variant names:

• chr5-51370784-A-G
• rs2115322

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 0.458 in 152,006 control chromosomes in the GnomAD database, including 17,888 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 0.46 (17888 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.120
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.689 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: 0.458 AC: 69603 AN: 151888 Hom.: 17851 Cov.: 32

Gnomad AFR AF: 0.695

Gnomad AMI AF: 0.365

Gnomad AMR AF: 0.383

Gnomad ASJ AF: 0.300

Gnomad EAS AF: 0.172

Gnomad SAS AF: 0.316

Gnomad FIN AF: 0.376

Gnomad MID AF: 0.344

Gnomad NFE AF: 0.387

Gnomad OTH AF: 0.419

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

GnomAD4 genome AF: 0.458 AC: 69689 AN: 152006 Hom.: 17888 Cov.: 32 AF XY: 0.450 AC XY: 33432 AN XY: 74324

African (AFR) AF: 0.696 AC: 28830 AN: 41448

American (AMR) AF: 0.383 AC: 5850 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.300 AC: 1042 AN: 3470

East Asian (EAS) AF: 0.173 AC: 893 AN: 5166

South Asian (SAS) AF: 0.315 AC: 1514 AN: 4810

European-Finnish (FIN) AF: 0.376 AC: 3974 AN: 10570

Middle Eastern (MID) AF: 0.332 AC: 97 AN: 292

European-Non Finnish (NFE) AF: 0.387 AC: 26282 AN: 67952

Other (OTH) AF: 0.415 AC: 875 AN: 2110

Alfa AF: 0.404 Hom.: 9554

Bravo AF: 0.469

Asia WGS AF: 0.308 AC: 1072 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.6
DANN	Benign	0.57
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs2115322; hg19: chr5-50666618;