15-92377797-C-T

Variant names:

• chr15-92377797-C-T
• rs4586379
• ENST00000838102.1:n.379-4933G>A

Variant summary

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

The ENST00000838102.1(ENSG00000309057):​n.379-4933G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.77 in 152,044 control chromosomes in the GnomAD database, including 45,206 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 0.77 (45206 hom., cov: 30)
• Consequence: ENSG00000309057 ENST00000838102.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0950
• Publications: 7 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=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.775 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000838102.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000309057	ENST00000838102.1		n.379-4933G>A		intron	N/A
	ENSG00000309057	ENST00000838103.1		n.412-4933G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.770 AC: 116937 AN: 151926 Hom.: 45142 Cov.: 30

Gnomad AFR AF: 0.762

Gnomad AMI AF: 0.719

Gnomad AMR AF: 0.784

Gnomad ASJ AF: 0.810

Gnomad EAS AF: 0.666

Gnomad SAS AF: 0.795

Gnomad FIN AF: 0.821

Gnomad MID AF: 0.799

Gnomad NFE AF: 0.768

Gnomad OTH AF: 0.775

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

GnomAD4 genome AF: 0.770 AC: 117063 AN: 152044 Hom.: 45206 Cov.: 30 AF XY: 0.773 AC XY: 57507 AN XY: 74348

African (AFR) AF: 0.762 AC: 31600 AN: 41446

American (AMR) AF: 0.784 AC: 11982 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.810 AC: 2809 AN: 3468

East Asian (EAS) AF: 0.667 AC: 3447 AN: 5170

South Asian (SAS) AF: 0.796 AC: 3841 AN: 4824

European-Finnish (FIN) AF: 0.821 AC: 8683 AN: 10578

Middle Eastern (MID) AF: 0.791 AC: 231 AN: 292

European-Non Finnish (NFE) AF: 0.768 AC: 52176 AN: 67968

Other (OTH) AF: 0.777 AC: 1638 AN: 2108

Alfa AF: 0.764 Hom.: 26246

Bravo AF: 0.766

Asia WGS AF: 0.772 AC: 2686 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.37
PhyloP100		-0.095

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4586379;

hg19: chr15-92921027;