rs4451923

Variant names:

• chr15-97395919-A-G
• rs4451923
• ENST00000558621.2:n.755+1738T>C

Variant summary

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

The ENST00000558621.2(LINC00923):​n.755+1738T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.479 in 151,976 control chromosomes in the GnomAD database, including 20,470 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 0.48 (20470 hom., cov: 32)
• Consequence: LINC00923 ENST00000558621.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17
• Publications: 5 publications found

Genes affected

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

LINC02253 (HGNC:53151): (long intergenic non-protein coding RNA 2253)

LINC02254 (HGNC:53152): (long intergenic non-protein coding RNA 2254)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.792 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02254	NR_120324.1	n.755+1738T>C		intron_variant	Intron 4 of 4
LINC02253	NR_183853.1	n.293-15273A>G		intron_variant	Intron 2 of 5
LINC02253	NR_183854.1	n.293-15273A>G		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00923	ENST00000558621.2	n.755+1738T>C		intron_variant	Intron 4 of 4	1
LINC00923	ENST00000658446.1	n.728T>C		non_coding_transcript_exon_variant	Exon 5 of 5
LINC00923	ENST00000740462.1	n.945T>C		non_coding_transcript_exon_variant	Exon 5 of 5

Frequencies

GnomAD3 genomes AF: 0.478 AC: 72634 AN: 151858 Hom.: 20426 Cov.: 32

Gnomad AFR AF: 0.799

Gnomad AMI AF: 0.330

Gnomad AMR AF: 0.426

Gnomad ASJ AF: 0.358

Gnomad EAS AF: 0.369

Gnomad SAS AF: 0.267

Gnomad FIN AF: 0.355

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.347

Gnomad OTH AF: 0.451

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

GnomAD4 genome AF: 0.479 AC: 72722 AN: 151976 Hom.: 20470 Cov.: 32 AF XY: 0.472 AC XY: 35098 AN XY: 74296

African (AFR) AF: 0.799 AC: 33152 AN: 41484

American (AMR) AF: 0.426 AC: 6499 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.358 AC: 1242 AN: 3468

East Asian (EAS) AF: 0.368 AC: 1900 AN: 5160

South Asian (SAS) AF: 0.265 AC: 1276 AN: 4822

European-Finnish (FIN) AF: 0.355 AC: 3754 AN: 10560

Middle Eastern (MID) AF: 0.384 AC: 113 AN: 294

European-Non Finnish (NFE) AF: 0.347 AC: 23543 AN: 67926

Other (OTH) AF: 0.447 AC: 943 AN: 2108

Alfa AF: 0.387 Hom.: 4388

Bravo AF: 0.502

Asia WGS AF: 0.341 AC: 1186 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.54
DANN	Benign	0.40
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs4451923; hg19: chr15-97939149;