4-19363093-C-G

Variant names:

• chr4-19363093-C-G
• rs982067
• ENST00000505347.1:n.350-29330G>C

Variant summary

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

The ENST00000505347.1(LINC02438):​n.350-29330G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.12 in 152,130 control chromosomes in the GnomAD database, including 1,464 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 0.12 (1464 hom., cov: 32)
• Consequence: LINC02438 ENST00000505347.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.212
• Publications: 1 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.216 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02438	XR_001741605.2	n.346-29330G>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02438	ENST00000505347.1	n.350-29330G>C		intron_variant	Intron 1 of 2	3
LINC02438	ENST00000669321.1	n.300-29330G>C		intron_variant	Intron 1 of 2
LINC02438	ENST00000796408.1	n.391-29330G>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.120 AC: 18255 AN: 152012 Hom.: 1461 Cov.: 32

Gnomad AFR AF: 0.219

Gnomad AMI AF: 0.0998

Gnomad AMR AF: 0.119

Gnomad ASJ AF: 0.102

Gnomad EAS AF: 0.226

Gnomad SAS AF: 0.0775

Gnomad FIN AF: 0.0608

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0663

Gnomad OTH AF: 0.112

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

GnomAD4 genome AF: 0.120 AC: 18298 AN: 152130 Hom.: 1464 Cov.: 32 AF XY: 0.122 AC XY: 9041 AN XY: 74372

African (AFR) AF: 0.219 AC: 9092 AN: 41492

American (AMR) AF: 0.119 AC: 1816 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.102 AC: 355 AN: 3468

East Asian (EAS) AF: 0.227 AC: 1169 AN: 5158

South Asian (SAS) AF: 0.0772 AC: 372 AN: 4820

European-Finnish (FIN) AF: 0.0608 AC: 644 AN: 10598

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.0663 AC: 4510 AN: 67994

Other (OTH) AF: 0.110 AC: 233 AN: 2112

Alfa AF: 0.0903 Hom.: 106

Bravo AF: 0.129

Asia WGS AF: 0.139 AC: 484 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.3
DANN	Benign	0.50
PhyloP100		0.21
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs982067; hg19: chr4-19364716;