15-92387181-G-A

Variant names:

• chr15-92387181-G-A
• rs17702901
• ENST00000838102.1:n.378+6883C>T

Variant summary

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

The ENST00000838102.1(ENSG00000309057):​n.378+6883C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.056 in 152,246 control chromosomes in the GnomAD database, including 436 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 0.056 (436 hom., cov: 33)
• Consequence: ENSG00000309057 ENST00000838102.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.78
• 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.152 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000309057	ENST00000838102.1		n.378+6883C>T		intron	N/A
	ENSG00000309057	ENST00000838103.1		n.411+5091C>T		intron	N/A
	ENSG00000309057	ENST00000838105.1		n.484-767C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0559 AC: 8504 AN: 152128 Hom.: 431 Cov.: 33

Gnomad AFR AF: 0.0435

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.156

Gnomad ASJ AF: 0.0239

Gnomad EAS AF: 0.141

Gnomad SAS AF: 0.118

Gnomad FIN AF: 0.0437

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0340

Gnomad OTH AF: 0.0612

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

GnomAD4 genome AF: 0.0560 AC: 8528 AN: 152246 Hom.: 436 Cov.: 33 AF XY: 0.0596 AC XY: 4436 AN XY: 74442

African (AFR) AF: 0.0433 AC: 1800 AN: 41538

American (AMR) AF: 0.157 AC: 2403 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0239 AC: 83 AN: 3470

East Asian (EAS) AF: 0.141 AC: 732 AN: 5180

South Asian (SAS) AF: 0.119 AC: 572 AN: 4824

European-Finnish (FIN) AF: 0.0437 AC: 464 AN: 10606

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0341 AC: 2316 AN: 68004

Other (OTH) AF: 0.0643 AC: 136 AN: 2114

Alfa AF: 0.0458 Hom.: 427

Bravo AF: 0.0649

Asia WGS AF: 0.150 AC: 519 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.0070
DANN	Benign	0.39
PhyloP100		-3.8

Splicing

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

Other links and lift over

dbSNP: rs17702901; hg19: chr15-92930411;