ENST00000846823.1:n.156+1064T>G

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105371019	XR_001751710.2	n.303+1064T>G		intron_variant	Intron 1 of 2
LOC105371019	XR_932714.3	n.258+1064T>G		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000310056	ENST00000846823.1	n.156+1064T>G		intron_variant	Intron 1 of 2
ENSG00000310056	ENST00000846824.1	n.165+1193T>G		intron_variant	Intron 1 of 2
ENSG00000310056	ENST00000846825.1	n.293+1064T>G		intron_variant	Intron 1 of 2
ENSG00000310056	ENST00000846826.1	n.137+1064T>G		intron_variant	Intron 1 of 1

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 v4.3

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

Other links and lift over

dbSNP: rs7175248; hg19: chr15-100048722;