rs4451923

Positions:

• chr15-97395919-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_120324.1(LINC02254):​n.755+1738T>C variant causes a intron, non coding transcript 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: LINC02254 NR_120324.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17

Genes affected

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

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LINC02254	NR_120324.1	n.755+1738T>C		intron_variant, non_coding_transcript_variant
LINC02253	NR_183855.1	n.448-15273A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02253	ENST00000559321.2	n.251-15273A>G		intron_variant, non_coding_transcript_variant		2
LINC02254	ENST00000653998.1	n.892+31732T>C		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.799

Gnomad4 AMR AF: 0.426

Gnomad4 ASJ AF: 0.358

Gnomad4 EAS AF: 0.368

Gnomad4 SAS AF: 0.265

Gnomad4 FIN AF: 0.355

Gnomad4 NFE AF: 0.347

Gnomad4 OTH AF: 0.447

Alfa AF: 0.401 Hom.: 3242

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4451923; hg19: chr15-97939149;