rs3759916

Variant names:

• chr15-92392939-C-T
• rs3759916

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 0.962 in 152,382 control chromosomes in the GnomAD database, including 70,963 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 0.96 (70963 hom., cov: 35)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.114

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.989 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: 0.962 AC: 146549 AN: 152264 Hom.: 70916 Cov.: 35

Gnomad AFR AF: 0.970

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.883

Gnomad ASJ AF: 0.995

Gnomad EAS AF: 0.651

Gnomad SAS AF: 0.929

Gnomad FIN AF: 0.995

Gnomad MID AF: 0.984

Gnomad NFE AF: 0.995

Gnomad OTH AF: 0.961

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

GnomAD4 genome AF: 0.962 AC: 146655 AN: 152382 Hom.: 70963 Cov.: 35 AF XY: 0.958 AC XY: 71395 AN XY: 74514

Gnomad4 AFR AF: 0.969

Gnomad4 AMR AF: 0.883

Gnomad4 ASJ AF: 0.995

Gnomad4 EAS AF: 0.652

Gnomad4 SAS AF: 0.929

Gnomad4 FIN AF: 0.995

Gnomad4 NFE AF: 0.995

Gnomad4 OTH AF: 0.959

Alfa AF: 0.986 Hom.: 16457

Bravo AF: 0.953

Asia WGS AF: 0.804 AC: 2798 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	11
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3759916; hg19: chr15-92936169;