rs8017950

chr14-100657531-G-A

Variant summary

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

The NR_024096.1(LINC00523):n.264G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.768 in 152,224 control chromosomes in the GnomAD database, including 48,212 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 0.77 (48210 hom., cov: 34)
  • Exomes 𝑓: 0.60 (2 hom.)
• Consequence: LINC00523 NR_024096.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.151

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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.941 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC00523	NR_024096.1	n.264G>A		non_coding_transcript_exon_variant	1/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00523	ENST00000360899.2	n.264G>A		non_coding_transcript_exon_variant	1/2	1
LINC00523	ENST00000556697.1	n.282G>A		non_coding_transcript_exon_variant	1/2	2
LINC00523	ENST00000553623.1	n.174G>A		non_coding_transcript_exon_variant	1/2	3

Frequencies

GnomAD3 genomes AF: 0.769 AC: 116907 AN: 152096 Hom.: 48208 Cov.: 34

Gnomad AFR AF: 0.526

Gnomad AMI AF: 0.969

Gnomad AMR AF: 0.653

Gnomad ASJ AF: 0.963

Gnomad EAS AF: 0.325

Gnomad SAS AF: 0.748

Gnomad FIN AF: 0.867

Gnomad MID AF: 0.924

Gnomad NFE AF: 0.947

Gnomad OTH AF: 0.808

GnomAD4 exome AF: 0.600 AC: 6 AN: 10 Hom.: 2 Cov.: 0 AF XY: 0.625 AC XY: 5 AN XY: 8

Gnomad4 EAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.667

Gnomad4 OTH exome AF: 1.00

GnomAD4 genome AF: 0.768 AC: 116941 AN: 152214 Hom.: 48210 Cov.: 34 AF XY: 0.761 AC XY: 56596 AN XY: 74412

Gnomad4 AFR AF: 0.526

Gnomad4 AMR AF: 0.652

Gnomad4 ASJ AF: 0.963

Gnomad4 EAS AF: 0.324

Gnomad4 SAS AF: 0.750

Gnomad4 FIN AF: 0.867

Gnomad4 NFE AF: 0.947

Gnomad4 OTH AF: 0.800

Alfa AF: 0.909 Hom.: 80115

Bravo AF: 0.738

Asia WGS AF: 0.517 AC: 1802 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	2.8
Dann	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8017950; hg19: chr14-101123868;