15-92393214-C-T

Variant names:

• chr15-92393214-C-T
• rs3759914

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 0.966 in 152,314 control chromosomes in the GnomAD database, including 71,439 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 0.97 (71439 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.119

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.991 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: 0.966 AC: 147024 AN: 152196 Hom.: 71380 Cov.: 33

Gnomad AFR AF: 0.972

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.890

Gnomad ASJ AF: 1.00

Gnomad EAS AF: 0.660

Gnomad SAS AF: 0.936

Gnomad FIN AF: 0.995

Gnomad MID AF: 0.997

Gnomad NFE AF: 0.998

Gnomad OTH AF: 0.972

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

GnomAD4 genome AF: 0.966 AC: 147141 AN: 152314 Hom.: 71439 Cov.: 33 AF XY: 0.962 AC XY: 71610 AN XY: 74474

Gnomad4 AFR AF: 0.972

Gnomad4 AMR AF: 0.889

Gnomad4 ASJ AF: 1.00

Gnomad4 EAS AF: 0.661

Gnomad4 SAS AF: 0.936

Gnomad4 FIN AF: 0.995

Gnomad4 NFE AF: 0.998

Gnomad4 OTH AF: 0.973

Alfa AF: 0.984 Hom.: 10768

Bravo AF: 0.957

Asia WGS AF: 0.835 AC: 2905 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	6.1
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3759914; hg19: chr15-92936444;