rs1951033

Positions:

• chr14-100668981-T-C

Variant summary

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

The NR_024096.1(LINC00523):​n.444-2580T>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 0.865 in 152,240 control chromosomes in the GnomAD database, including 58,465 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 0.87 (58465 hom., cov: 32)
• Consequence: LINC00523 NR_024096.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.998

Genes affected

LINC00523 (HGNC:20117): (long intergenic non-protein coding RNA 523)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.968 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC00523	NR_024096.1	n.444-2580T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00523	ENST00000556697.1	n.857-2580T>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.865 AC: 131624 AN: 152122 Hom.: 58429 Cov.: 32

Gnomad AFR AF: 0.754

Gnomad AMI AF: 0.971

Gnomad AMR AF: 0.732

Gnomad ASJ AF: 0.988

Gnomad EAS AF: 0.450

Gnomad SAS AF: 0.920

Gnomad FIN AF: 0.915

Gnomad MID AF: 0.968

Gnomad NFE AF: 0.974

Gnomad OTH AF: 0.886

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

GnomAD4 genome AF: 0.865 AC: 131701 AN: 152240 Hom.: 58465 Cov.: 32 AF XY: 0.859 AC XY: 63928 AN XY: 74434

Gnomad4 AFR AF: 0.754

Gnomad4 AMR AF: 0.731

Gnomad4 ASJ AF: 0.988

Gnomad4 EAS AF: 0.450

Gnomad4 SAS AF: 0.922

Gnomad4 FIN AF: 0.915

Gnomad4 NFE AF: 0.974

Gnomad4 OTH AF: 0.879

Alfa AF: 0.943 Hom.: 111091

Bravo AF: 0.843

Asia WGS AF: 0.675 AC: 2350 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.28
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1951033; hg19: chr14-101135318;