rs393974

chr15-90818771-C-Achr15-90818771-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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;