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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000505347.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02438	ENST00000505347.1	TSL:3	n.450-76284G>C		intron	N/A
	LINC02438	ENST00000669321.1		n.400-29947G>C		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs312364;

hg19: chr4-19250433;