chr4-129861637-C-G

Variant names:

• chr4-129861637-C-G
• rs2969001
• ENST00000507099.1:n.66-931C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000507099.1(LINC02465):​n.66-931C>G variant causes a intron 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 ENST00000507099.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.257
• Publications: 6 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LINC02465	NR_151713.1	n.987-931C>G		intron_variant	Intron 10 of 16

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02465	ENST00000507099.1	n.66-931C>G		intron_variant	Intron 1 of 3	4
LINC02465	ENST00000513875.5	n.947-931C>G		intron_variant	Intron 10 of 16	5
LINC02465	ENST00000652794.1	n.1025-931C>G		intron_variant	Intron 8 of 11

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

African (AFR) AF: 0.200 AC: 8279 AN: 41496

American (AMR) AF: 0.463 AC: 7060 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.537 AC: 1861 AN: 3464

East Asian (EAS) AF: 0.272 AC: 1403 AN: 5156

South Asian (SAS) AF: 0.366 AC: 1761 AN: 4818

European-Finnish (FIN) AF: 0.636 AC: 6713 AN: 10552

Middle Eastern (MID) AF: 0.524 AC: 154 AN: 294

European-Non Finnish (NFE) AF: 0.675 AC: 45849 AN: 67908

Other (OTH) AF: 0.491 AC: 1032 AN: 2102

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
PhyloP100		0.26

Splicing

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

Other links and lift over

dbSNP: rs2969001; hg19: chr4-130782792;