4-19248810-C-G

Variant names:

• chr4-19248810-C-G
• rs312364
• ENST00000505347.1:n.450-76284G>C

Variant summary

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

The ENST00000505347.1(LINC02438):​n.450-76284G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.5 in 151,898 control chromosomes in the GnomAD database, including 19,347 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 (19347 hom., cov: 31)
• Consequence: LINC02438 ENST00000505347.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.305
• Publications: 0 publications found

Genes affected

LINC02438 (HGNC:53370): (long intergenic non-protein coding RNA 2438)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.576 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02438	XR_001741605.2	n.446-29947G>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02438	ENST00000505347.1	n.450-76284G>C		intron_variant	Intron 2 of 2	3
LINC02438	ENST00000669321.1	n.400-29947G>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.500 AC: 75899 AN: 151778 Hom.: 19328 Cov.: 31

Gnomad AFR AF: 0.542

Gnomad AMI AF: 0.527

Gnomad AMR AF: 0.586

Gnomad ASJ AF: 0.493

Gnomad EAS AF: 0.546

Gnomad SAS AF: 0.450

Gnomad FIN AF: 0.578

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.444

Gnomad OTH AF: 0.499

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

GnomAD4 genome AF: 0.500 AC: 75947 AN: 151898 Hom.: 19347 Cov.: 31 AF XY: 0.506 AC XY: 37514 AN XY: 74198

African (AFR) AF: 0.541 AC: 22423 AN: 41438

American (AMR) AF: 0.587 AC: 8958 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.493 AC: 1709 AN: 3468

East Asian (EAS) AF: 0.545 AC: 2788 AN: 5118

South Asian (SAS) AF: 0.451 AC: 2170 AN: 4810

European-Finnish (FIN) AF: 0.578 AC: 6088 AN: 10534

Middle Eastern (MID) AF: 0.380 AC: 111 AN: 292

European-Non Finnish (NFE) AF: 0.444 AC: 30165 AN: 67940

Other (OTH) AF: 0.499 AC: 1055 AN: 2116

Alfa AF: 0.319 Hom.: 780

Bravo AF: 0.506

Asia WGS AF: 0.504 AC: 1750 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.9
DANN	Benign	0.60
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs312364; hg19: chr4-19250433;