rs11099284

Positions:

• chr4-134517569-T-C

Variant summary

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

The NR_147155.1(LINC02462):​n.430-27717T>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 0.772 in 152,098 control chromosomes in the GnomAD database, including 45,769 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 (45769 hom., cov: 32)
• Consequence: LINC02462 NR_147155.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0700

Genes affected

LINC02462 (HGNC:53399): (long intergenic non-protein coding RNA 2462)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.959 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02462	NR_147155.1	n.430-27717T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02462	ENST00000666281.1	n.485-27717T>C		intron_variant, non_coding_transcript_variant
LINC02462	ENST00000666371.1	n.314-27717T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.772 AC: 117280 AN: 151980 Hom.: 45725 Cov.: 32

Gnomad AFR AF: 0.668

Gnomad AMI AF: 0.761

Gnomad AMR AF: 0.756

Gnomad ASJ AF: 0.789

Gnomad EAS AF: 0.981

Gnomad SAS AF: 0.698

Gnomad FIN AF: 0.797

Gnomad MID AF: 0.783

Gnomad NFE AF: 0.822

Gnomad OTH AF: 0.803

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

GnomAD4 genome AF: 0.772 AC: 117375 AN: 152098 Hom.: 45769 Cov.: 32 AF XY: 0.770 AC XY: 57220 AN XY: 74338

Gnomad4 AFR AF: 0.668

Gnomad4 AMR AF: 0.756

Gnomad4 ASJ AF: 0.789

Gnomad4 EAS AF: 0.981

Gnomad4 SAS AF: 0.700

Gnomad4 FIN AF: 0.797

Gnomad4 NFE AF: 0.822

Gnomad4 OTH AF: 0.805

Alfa AF: 0.815 Hom.: 97094

Bravo AF: 0.767

Asia WGS AF: 0.821 AC: 2854 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.2
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11099284; hg19: chr4-135438724;