4-129810129-T-C

Position:

• chr4-129810129-T-C

Variant summary

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

The NR_151713.1(LINC02465):​n.429-1873T>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 0.485 in 151,926 control chromosomes in the GnomAD database, including 20,615 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 (20615 hom., cov: 32)
• Consequence: LINC02465 NR_151713.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.184

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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.646 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02465	NR_151713.1	n.429-1873T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02465	ENST00000658130.1	n.183-1873T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.485 AC: 73634 AN: 151808 Hom.: 20625 Cov.: 32

Gnomad AFR AF: 0.219

Gnomad AMI AF: 0.557

Gnomad AMR AF: 0.466

Gnomad ASJ AF: 0.505

Gnomad EAS AF: 0.270

Gnomad SAS AF: 0.462

Gnomad FIN AF: 0.591

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.651

Gnomad OTH AF: 0.492

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

GnomAD4 genome AF: 0.485 AC: 73635 AN: 151926 Hom.: 20615 Cov.: 32 AF XY: 0.481 AC XY: 35706 AN XY: 74226

Gnomad4 AFR AF: 0.219

Gnomad4 AMR AF: 0.466

Gnomad4 ASJ AF: 0.505

Gnomad4 EAS AF: 0.271

Gnomad4 SAS AF: 0.461

Gnomad4 FIN AF: 0.591

Gnomad4 NFE AF: 0.651

Gnomad4 OTH AF: 0.486

Alfa AF: 0.612 Hom.: 34370

Bravo AF: 0.461

Asia WGS AF: 0.318 AC: 1104 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.3
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4864201; hg19: chr4-130731284;