rs2388881

Variant names:

• chr15-94740138-A-C
• rs2388881

Your query was ambiguous. Multiple possible variants found:

• chr15-94740138-A-C
• chr15-94740138-A-G

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 0.576 in 151,964 control chromosomes in the GnomAD database, including 26,628 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 0.58 (26628 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.362
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.781 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.576 AC: 87398 AN: 151846 Hom.: 26603 Cov.: 31

Gnomad AFR AF: 0.370

Gnomad AMI AF: 0.645

Gnomad AMR AF: 0.688

Gnomad ASJ AF: 0.655

Gnomad EAS AF: 0.801

Gnomad SAS AF: 0.683

Gnomad FIN AF: 0.643

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.634

Gnomad OTH AF: 0.602

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

GnomAD4 genome AF: 0.576 AC: 87463 AN: 151964 Hom.: 26628 Cov.: 31 AF XY: 0.583 AC XY: 43301 AN XY: 74260

African (AFR) AF: 0.370 AC: 15349 AN: 41436

American (AMR) AF: 0.689 AC: 10527 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.655 AC: 2269 AN: 3462

East Asian (EAS) AF: 0.802 AC: 4146 AN: 5172

South Asian (SAS) AF: 0.684 AC: 3294 AN: 4814

European-Finnish (FIN) AF: 0.643 AC: 6767 AN: 10528

Middle Eastern (MID) AF: 0.493 AC: 145 AN: 294

European-Non Finnish (NFE) AF: 0.635 AC: 43119 AN: 67956

Other (OTH) AF: 0.597 AC: 1260 AN: 2112

Alfa AF: 0.607 Hom.: 46289

Bravo AF: 0.570

Asia WGS AF: 0.660 AC: 2291 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.0
DANN	Benign	0.58
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs2388881; hg19: chr15-95283367;