15-97617014-C-T

Variant names:

• chr15-97617014-C-T
• rs11631323
• ENST00000615399.1:n.411+35038G>A

Variant summary

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

The ENST00000658023.1(LINC00923):​n.357+35038G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.238 in 151,958 control chromosomes in the GnomAD database, including 4,576 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 0.24 (4576 hom., cov: 32)
• Consequence: LINC00923 ENST00000658023.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.139
• Publications: 7 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.361 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000658023.1. 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	ENST00000615399.1	TSL:5	n.411+35038G>A		intron	N/A
	LINC00923	ENST00000658023.1		n.357+35038G>A		intron	N/A
	LINC00923	ENST00000715390.1		n.598+35038G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.238 AC: 36152 AN: 151840 Hom.: 4559 Cov.: 32

Gnomad AFR AF: 0.258

Gnomad AMI AF: 0.311

Gnomad AMR AF: 0.262

Gnomad ASJ AF: 0.149

Gnomad EAS AF: 0.375

Gnomad SAS AF: 0.287

Gnomad FIN AF: 0.269

Gnomad MID AF: 0.109

Gnomad NFE AF: 0.206

Gnomad OTH AF: 0.222

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

GnomAD4 genome AF: 0.238 AC: 36195 AN: 151958 Hom.: 4576 Cov.: 32 AF XY: 0.241 AC XY: 17918 AN XY: 74266

African (AFR) AF: 0.258 AC: 10683 AN: 41426

American (AMR) AF: 0.263 AC: 4021 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.149 AC: 518 AN: 3466

East Asian (EAS) AF: 0.375 AC: 1933 AN: 5160

South Asian (SAS) AF: 0.286 AC: 1380 AN: 4820

European-Finnish (FIN) AF: 0.269 AC: 2838 AN: 10542

Middle Eastern (MID) AF: 0.114 AC: 33 AN: 290

European-Non Finnish (NFE) AF: 0.206 AC: 14024 AN: 67960

Other (OTH) AF: 0.229 AC: 483 AN: 2106

Alfa AF: 0.206 Hom.: 7003

Bravo AF: 0.236

Asia WGS AF: 0.347 AC: 1206 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.5
DANN	Benign	0.44
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs11631323; hg19: chr15-98160244;