4-188766243-C-T

Variant names:

• chr4-188766243-C-T
• rs4863387
• ENST00000505178.2:n.68-2548C>T

Variant summary

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

The ENST00000505178.2(LINC02508):​n.68-2548C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.502 in 151,950 control chromosomes in the GnomAD database, including 20,415 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 0.50 (20415 hom., cov: 33)
• Consequence: LINC02508 ENST00000505178.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.328
• Publications: 2 publications found

Genes affected

LINC02508 (HGNC:53497): (long intergenic non-protein coding RNA 2508)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.77 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000505178.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02508	ENST00000505178.2	TSL:3	n.68-2548C>T		intron	N/A
	LINC02508	ENST00000717494.1		n.46-2548C>T		intron	N/A
	LINC02508	ENST00000717495.1		n.143+196C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.502 AC: 76196 AN: 151834 Hom.: 20426 Cov.: 33

Gnomad AFR AF: 0.314

Gnomad AMI AF: 0.686

Gnomad AMR AF: 0.551

Gnomad ASJ AF: 0.554

Gnomad EAS AF: 0.790

Gnomad SAS AF: 0.495

Gnomad FIN AF: 0.591

Gnomad MID AF: 0.580

Gnomad NFE AF: 0.563

Gnomad OTH AF: 0.533

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

GnomAD4 genome AF: 0.502 AC: 76208 AN: 151950 Hom.: 20415 Cov.: 33 AF XY: 0.507 AC XY: 37688 AN XY: 74284

African (AFR) AF: 0.314 AC: 13003 AN: 41440

American (AMR) AF: 0.551 AC: 8405 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.554 AC: 1922 AN: 3468

East Asian (EAS) AF: 0.790 AC: 4071 AN: 5152

South Asian (SAS) AF: 0.495 AC: 2385 AN: 4814

European-Finnish (FIN) AF: 0.591 AC: 6241 AN: 10552

Middle Eastern (MID) AF: 0.568 AC: 166 AN: 292

European-Non Finnish (NFE) AF: 0.563 AC: 38271 AN: 67946

Other (OTH) AF: 0.530 AC: 1120 AN: 2112

Alfa AF: 0.536 Hom.: 49156

Bravo AF: 0.493

Asia WGS AF: 0.596 AC: 2063 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.69
DANN	Benign	0.65
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs4863387; hg19: chr4-189687397;