rs3759916

chr15-92392939-C-T

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/exons	MANE	UniProt

Ensembl

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