15-97550004-C-T

Variant names:

• chr15-97550004-C-T
• rs1500652
• ENST00000715390.1:n.797-8256G>A

Variant summary

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

The ENST00000715390.1(LINC00923):​n.797-8256G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.327 in 151,404 control chromosomes in the GnomAD database, including 12,233 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 0.33 (12233 hom., cov: 32)
• Consequence: LINC00923 ENST00000715390.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.932
• Publications: 6 publications found

Genes affected

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=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.708 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000715390.1. 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
	LINC00923	ENST00000715390.1		n.797-8256G>A		intron	N/A
	LINC00923	ENST00000715695.1		n.420-8256G>A		intron	N/A
	LINC00923	ENST00000740435.1		n.725+8897G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.326 AC: 49374 AN: 151286 Hom.: 12183 Cov.: 32

Gnomad AFR AF: 0.640

Gnomad AMI AF: 0.180

Gnomad AMR AF: 0.310

Gnomad ASJ AF: 0.122

Gnomad EAS AF: 0.728

Gnomad SAS AF: 0.365

Gnomad FIN AF: 0.222

Gnomad MID AF: 0.150

Gnomad NFE AF: 0.136

Gnomad OTH AF: 0.296

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

GnomAD4 genome AF: 0.327 AC: 49493 AN: 151404 Hom.: 12233 Cov.: 32 AF XY: 0.332 AC XY: 24555 AN XY: 73946

African (AFR) AF: 0.641 AC: 26493 AN: 41360

American (AMR) AF: 0.311 AC: 4728 AN: 15210

Ashkenazi Jewish (ASJ) AF: 0.122 AC: 423 AN: 3466

East Asian (EAS) AF: 0.728 AC: 3756 AN: 5162

South Asian (SAS) AF: 0.365 AC: 1754 AN: 4802

European-Finnish (FIN) AF: 0.222 AC: 2299 AN: 10358

Middle Eastern (MID) AF: 0.154 AC: 45 AN: 292

European-Non Finnish (NFE) AF: 0.136 AC: 9197 AN: 67750

Other (OTH) AF: 0.303 AC: 635 AN: 2096

Alfa AF: 0.192 Hom.: 2563

Bravo AF: 0.354

Asia WGS AF: 0.565 AC: 1951 AN: 3456

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.59
DANN	Benign	0.18
PhyloP100		-0.93

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: rs1500652;

hg19: chr15-98093234;