ENST00000658524.1:n.227-2185A>G

Variant names:

• chr15-97570321-A-G
• rs288392
• ENST00000658524.1:n.227-2185A>G

Variant summary

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

The ENST00000658524.1(ENSG00000287321):​n.227-2185A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.636 in 151,954 control chromosomes in the GnomAD database, including 31,215 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 0.64 (31215 hom., cov: 32)
• Consequence: ENSG00000287321 ENST00000658524.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.803
• Publications: 2 publications found

Genes affected

ENSG00000287321 (HGNC:):

LINC00923 (HGNC:28088): (long intergenic non-protein coding RNA 923)

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 (AFR) allele frequency at 95% confidence interval = 0.732 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287321	ENST00000658524.1	n.227-2185A>G		intron_variant	Intron 3 of 3
LINC00923	ENST00000715390.1	n.599-11223T>C		intron_variant	Intron 4 of 6
LINC00923	ENST00000715695.1	n.420-28573T>C		intron_variant	Intron 3 of 7

Frequencies

GnomAD3 genomes AF: 0.636 AC: 96511 AN: 151836 Hom.: 31192 Cov.: 32

Gnomad AFR AF: 0.738

Gnomad AMI AF: 0.576

Gnomad AMR AF: 0.636

Gnomad ASJ AF: 0.684

Gnomad EAS AF: 0.564

Gnomad SAS AF: 0.717

Gnomad FIN AF: 0.533

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.587

Gnomad OTH AF: 0.633

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

GnomAD4 genome AF: 0.636 AC: 96580 AN: 151954 Hom.: 31215 Cov.: 32 AF XY: 0.636 AC XY: 47275 AN XY: 74276

African (AFR) AF: 0.738 AC: 30628 AN: 41474

American (AMR) AF: 0.636 AC: 9701 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.684 AC: 2371 AN: 3464

East Asian (EAS) AF: 0.564 AC: 2905 AN: 5148

South Asian (SAS) AF: 0.717 AC: 3449 AN: 4810

European-Finnish (FIN) AF: 0.533 AC: 5630 AN: 10560

Middle Eastern (MID) AF: 0.690 AC: 203 AN: 294

European-Non Finnish (NFE) AF: 0.587 AC: 39845 AN: 67924

Other (OTH) AF: 0.628 AC: 1324 AN: 2108

Alfa AF: 0.493 Hom.: 1360

Bravo AF: 0.645

Asia WGS AF: 0.659 AC: 2289 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.40
PhyloP100		-0.80

Splicing

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

Other links and lift over

dbSNP: rs288392; hg19: chr15-98113551;