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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.603

Gnomad4 AMR AF: 0.700

Gnomad4 ASJ AF: 0.655

Gnomad4 EAS AF: 0.810

Gnomad4 SAS AF: 0.610

Gnomad4 FIN AF: 0.557

Gnomad4 NFE AF: 0.603

Gnomad4 OTH AF: 0.619

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

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