rs393974

Variant names:

• chr15-90818771-C-A
• rs393974

Your query was ambiguous. Multiple possible variants found:

• chr15-90818771-C-A
• chr15-90818771-C-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 0.619 in 152,032 control chromosomes in the GnomAD database, including 29,443 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 0.62 (29443 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.229
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.789 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: 0.619 AC: 94024 AN: 151914 Hom.: 29399 Cov.: 33

Gnomad AFR AF: 0.603

Gnomad AMI AF: 0.738

Gnomad AMR AF: 0.699

Gnomad ASJ AF: 0.655

Gnomad EAS AF: 0.810

Gnomad SAS AF: 0.610

Gnomad FIN AF: 0.557

Gnomad MID AF: 0.582

Gnomad NFE AF: 0.603

Gnomad OTH AF: 0.618

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

GnomAD4 genome AF: 0.619 AC: 94129 AN: 152032 Hom.: 29443 Cov.: 33 AF XY: 0.619 AC XY: 45981 AN XY: 74312

African (AFR) AF: 0.603 AC: 25034 AN: 41486

American (AMR) AF: 0.700 AC: 10698 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.655 AC: 2272 AN: 3468

East Asian (EAS) AF: 0.810 AC: 4180 AN: 5162

South Asian (SAS) AF: 0.610 AC: 2942 AN: 4822

European-Finnish (FIN) AF: 0.557 AC: 5879 AN: 10560

Middle Eastern (MID) AF: 0.578 AC: 170 AN: 294

European-Non Finnish (NFE) AF: 0.603 AC: 40972 AN: 67930

Other (OTH) AF: 0.619 AC: 1309 AN: 2114

Alfa AF: 0.525 Hom.: 1579

Bravo AF: 0.631

Asia WGS AF: 0.697 AC: 2424 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.92
DANN	Benign	0.63
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs393974; hg19: chr15-91362001; COSMIC: COSV61922747;