4-129861637-C-G

Position:

• chr4-129861637-C-G

Variant summary

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

The NR_151713.1(LINC02465):​n.987-931C>G 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 0.491 in 151,930 control chromosomes in the GnomAD database, including 21,720 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 0.49 (21720 hom., cov: 31)
• Consequence: LINC02465 NR_151713.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.257

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 = 0.67 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02465	NR_151713.1	n.987-931C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02465	ENST00000658130.1	n.741-969C>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.491 AC: 74606 AN: 151812 Hom.: 21727 Cov.: 31

Gnomad AFR AF: 0.200

Gnomad AMI AF: 0.548

Gnomad AMR AF: 0.464

Gnomad ASJ AF: 0.537

Gnomad EAS AF: 0.271

Gnomad SAS AF: 0.365

Gnomad FIN AF: 0.636

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.675

Gnomad OTH AF: 0.497

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

GnomAD4 genome AF: 0.491 AC: 74610 AN: 151930 Hom.: 21720 Cov.: 31 AF XY: 0.486 AC XY: 36109 AN XY: 74258

Gnomad4 AFR AF: 0.200

Gnomad4 AMR AF: 0.463

Gnomad4 ASJ AF: 0.537

Gnomad4 EAS AF: 0.272

Gnomad4 SAS AF: 0.366

Gnomad4 FIN AF: 0.636

Gnomad4 NFE AF: 0.675

Gnomad4 OTH AF: 0.491

Alfa AF: 0.450 Hom.: 1506

Bravo AF: 0.465

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.7
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2969001; hg19: chr4-130782792;