15-92393214-C-T

Variant names:

• chr15-92393214-C-T
• rs3759914
• ENST00000838102.1:n.378+850G>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+850G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: ENSG00000309057 ENST00000838102.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.119
• Publications: 9 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=-0.81).
• 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
ENSG00000309057	ENST00000838102.1	n.378+850G>A		intron_variant	Intron 1 of 9
ENSG00000309057	ENST00000838105.1	n.483+850G>A		intron_variant	Intron 1 of 1

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

African (AFR) AF: 0.972 AC: 40433 AN: 41582

American (AMR) AF: 0.889 AC: 13609 AN: 15308

Ashkenazi Jewish (ASJ) AF: 1.00 AC: 3472 AN: 3472

East Asian (EAS) AF: 0.661 AC: 3399 AN: 5142

South Asian (SAS) AF: 0.936 AC: 4512 AN: 4820

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

Middle Eastern (MID) AF: 0.997 AC: 293 AN: 294

European-Non Finnish (NFE) AF: 0.998 AC: 67885 AN: 68044

Other (OTH) AF: 0.973 AC: 2056 AN: 2114

Alfa AF: 0.980 Hom.: 18075

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
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs3759914; hg19: chr15-92936444;