rs10518558

chr4-129918495-G-T

Variant summary

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

The NR_151713.1(LINC02465):n.1374+9792G>T 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 0.0376 in 152,178 control chromosomes in the GnomAD database, including 289 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 0.038 (289 hom., cov: 33)
• Consequence: LINC02465 NR_151713.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.703

Genes affected

LINC02465 (HGNC:53403): (long intergenic non-protein coding RNA 2465)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.158 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02465	NR_151713.1	n.1374+9792G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02465	ENST00000658130.1	n.1090+9792G>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0374 AC: 5692 AN: 152060 Hom.: 286 Cov.: 33

Gnomad AFR AF: 0.0255

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0894

Gnomad ASJ AF: 0.00980

Gnomad EAS AF: 0.167

Gnomad SAS AF: 0.114

Gnomad FIN AF: 0.0862

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0121

Gnomad OTH AF: 0.0382

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

GnomAD4 genome AF: 0.0376 AC: 5723 AN: 152178 Hom.: 289 Cov.: 33 AF XY: 0.0441 AC XY: 3282 AN XY: 74392

Gnomad4 AFR AF: 0.0257

Gnomad4 AMR AF: 0.0897

Gnomad4 ASJ AF: 0.00980

Gnomad4 EAS AF: 0.167

Gnomad4 SAS AF: 0.114

Gnomad4 FIN AF: 0.0862

Gnomad4 NFE AF: 0.0121

Gnomad4 OTH AF: 0.0440

Alfa AF: 0.0336 Hom.: 32

Bravo AF: 0.0365

Asia WGS AF: 0.174 AC: 605 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	2.8
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: rs10518558; hg19: chr4-130839650;