chr15-99508517-A-C

Variant names:

• chr15-99508517-A-C
• rs7175248
• ENST00000846823.1:n.156+1064T>G

Variant summary

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

The ENST00000846823.1(ENSG00000310056):​n.156+1064T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.565 in 152,150 control chromosomes in the GnomAD database, including 24,751 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 0.56 (24751 hom., cov: 33)
• Consequence: ENSG00000310056 ENST00000846823.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.803
• Publications: 5 publications found

Genes affected

ENSG00000310056 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.623 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000846823.1. 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
	ENSG00000310056	ENST00000846823.1		n.156+1064T>G		intron	N/A
	ENSG00000310056	ENST00000846824.1		n.165+1193T>G		intron	N/A
	ENSG00000310056	ENST00000846825.1		n.293+1064T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.565 AC: 85826 AN: 152032 Hom.: 24724 Cov.: 33

Gnomad AFR AF: 0.630

Gnomad AMI AF: 0.761

Gnomad AMR AF: 0.516

Gnomad ASJ AF: 0.617

Gnomad EAS AF: 0.325

Gnomad SAS AF: 0.487

Gnomad FIN AF: 0.383

Gnomad MID AF: 0.739

Gnomad NFE AF: 0.581

Gnomad OTH AF: 0.575

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

GnomAD4 genome AF: 0.565 AC: 85900 AN: 152150 Hom.: 24751 Cov.: 33 AF XY: 0.551 AC XY: 40994 AN XY: 74378

African (AFR) AF: 0.630 AC: 26144 AN: 41528

American (AMR) AF: 0.516 AC: 7887 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.617 AC: 2141 AN: 3470

East Asian (EAS) AF: 0.325 AC: 1682 AN: 5172

South Asian (SAS) AF: 0.487 AC: 2351 AN: 4826

European-Finnish (FIN) AF: 0.383 AC: 4052 AN: 10576

Middle Eastern (MID) AF: 0.743 AC: 217 AN: 292

European-Non Finnish (NFE) AF: 0.581 AC: 39525 AN: 67974

Other (OTH) AF: 0.571 AC: 1207 AN: 2112

Alfa AF: 0.576 Hom.: 102360

Bravo AF: 0.576

Asia WGS AF: 0.424 AC: 1471 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	7.0
DANN	Benign	0.59
PhyloP100		0.80
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: rs7175248;

hg19: chr15-100048722;