15-99495231-C-G

Variant names:

• chr15-99495231-C-G
• rs7181055
• ENST00000846715.1:n.196+4008C>G

Variant summary

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

The ENST00000846715.1(ENSG00000310039):​n.196+4008C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.245 in 152,188 control chromosomes in the GnomAD database, including 5,075 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 0.25 (5075 hom., cov: 33)
• Consequence: ENSG00000310039 ENST00000846715.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.369
• Publications: 0 publications found

Genes affected

ENSG00000310039 (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 (EAS) allele frequency at 95% confidence interval = 0.533 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000846715.1. 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
	ENSG00000310039	ENST00000846715.1		n.196+4008C>G		intron	N/A
	ENSG00000310039	ENST00000846717.1		n.186+4008C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.245 AC: 37333 AN: 152070 Hom.: 5081 Cov.: 33

Gnomad AFR AF: 0.286

Gnomad AMI AF: 0.0669

Gnomad AMR AF: 0.225

Gnomad ASJ AF: 0.202

Gnomad EAS AF: 0.550

Gnomad SAS AF: 0.413

Gnomad FIN AF: 0.275

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.191

Gnomad OTH AF: 0.225

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

GnomAD4 genome AF: 0.245 AC: 37332 AN: 152188 Hom.: 5075 Cov.: 33 AF XY: 0.252 AC XY: 18782 AN XY: 74396

African (AFR) AF: 0.285 AC: 11840 AN: 41516

American (AMR) AF: 0.225 AC: 3442 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.202 AC: 703 AN: 3472

East Asian (EAS) AF: 0.550 AC: 2836 AN: 5158

South Asian (SAS) AF: 0.413 AC: 1987 AN: 4816

European-Finnish (FIN) AF: 0.275 AC: 2919 AN: 10604

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.191 AC: 13019 AN: 68012

Other (OTH) AF: 0.226 AC: 476 AN: 2106

Alfa AF: 0.0579 Hom.: 63

Bravo AF: 0.243

Asia WGS AF: 0.486 AC: 1689 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	0.44
DANN	Benign	0.65
PhyloP100		-0.37
Mutation Taster		=100/0	polymorphism (auto)

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: rs7181055;

hg19: chr15-100035436;