rs3759916

Variant names:

• chr15-92392939-C-T
• rs3759916
• ENST00000838102.1:n.378+1125G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000838102.1(ENSG00000309057):​n.378+1125G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: ENSG00000309057 ENST00000838102.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.114
• Publications: 10 publications found

Genes affected

ENSG00000309057 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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
ENSG00000309057	ENST00000838102.1	n.378+1125G>A		intron_variant	Intron 1 of 9
ENSG00000309057	ENST00000838105.1	n.483+1125G>A		intron_variant	Intron 1 of 1

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

African (AFR) AF: 0.969 AC: 40327 AN: 41596

American (AMR) AF: 0.883 AC: 13517 AN: 15312

Ashkenazi Jewish (ASJ) AF: 0.995 AC: 3456 AN: 3472

East Asian (EAS) AF: 0.652 AC: 3373 AN: 5176

South Asian (SAS) AF: 0.929 AC: 4488 AN: 4832

European-Finnish (FIN) AF: 0.995 AC: 10572 AN: 10628

Middle Eastern (MID) AF: 0.983 AC: 289 AN: 294

European-Non Finnish (NFE) AF: 0.995 AC: 67691 AN: 68044

Other (OTH) AF: 0.959 AC: 2030 AN: 2116

Alfa AF: 0.982 Hom.: 33929

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
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs3759916; hg19: chr15-92936169;