chr15-97539048-T-C

Variant names:

• chr15-97539048-T-C
• rs12912857
• ENST00000715695.1:n.528+2592A>G

Variant summary

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

The ENST00000715695.1(LINC00923):​n.528+2592A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.708 in 152,098 control chromosomes in the GnomAD database, including 38,738 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 0.71 (38715 hom., cov: 31)
  • Exomes 𝑓: 0.68 (23 hom.)
• Consequence: LINC00923 ENST00000715695.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.89
• Publications: 4 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=-1.05).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.872 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000715695.1. 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	ENST00000715695.1		n.528+2592A>G		intron	N/A
	LINC00923	ENST00000740435.1		n.725+19853A>G		intron	N/A
	LINC00923	ENST00000740436.1		n.526+19853A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.708 AC: 107573 AN: 151874 Hom.: 38665 Cov.: 31

Gnomad AFR AF: 0.801

Gnomad AMI AF: 0.599

Gnomad AMR AF: 0.727

Gnomad ASJ AF: 0.641

Gnomad EAS AF: 0.894

Gnomad SAS AF: 0.764

Gnomad FIN AF: 0.765

Gnomad MID AF: 0.633

Gnomad NFE AF: 0.626

Gnomad OTH AF: 0.700

GnomAD4 exome AF: 0.679 AC: 72 AN: 106 Hom.: 23 Cov.: 0 AF XY: 0.700 AC XY: 63 AN XY: 90

African (AFR) AF: 1.00 AC: 4 AN: 4

American (AMR) AF: 0.667 AC: 4 AN: 6

Ashkenazi Jewish (ASJ) AF: 0.500 AC: 1 AN: 2

East Asian (EAS) AF: 1.00 AC: 2 AN: 2

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.659 AC: 58 AN: 88

Other (OTH) AF: 0.750 AC: 3 AN: 4

GnomAD4 genome AF: 0.708 AC: 107684 AN: 151992 Hom.: 38715 Cov.: 31 AF XY: 0.717 AC XY: 53289 AN XY: 74282

African (AFR) AF: 0.801 AC: 33223 AN: 41474

American (AMR) AF: 0.727 AC: 11117 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.641 AC: 2224 AN: 3468

East Asian (EAS) AF: 0.894 AC: 4592 AN: 5138

South Asian (SAS) AF: 0.765 AC: 3674 AN: 4802

European-Finnish (FIN) AF: 0.765 AC: 8088 AN: 10578

Middle Eastern (MID) AF: 0.636 AC: 187 AN: 294

European-Non Finnish (NFE) AF: 0.626 AC: 42553 AN: 67938

Other (OTH) AF: 0.703 AC: 1481 AN: 2108

Alfa AF: 0.682 Hom.: 6546

Bravo AF: 0.715

Asia WGS AF: 0.813 AC: 2829 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.17
DANN	Benign	0.36
PhyloP100		-1.9

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: rs12912857;

hg19: chr15-98082278;