4-19363093-C-G

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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

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

Gnomad4 AFR AF: 0.219

Gnomad4 AMR AF: 0.119

Gnomad4 ASJ AF: 0.102

Gnomad4 EAS AF: 0.227

Gnomad4 SAS AF: 0.0772

Gnomad4 FIN AF: 0.0608

Gnomad4 NFE AF: 0.0663

Gnomad4 OTH AF: 0.110

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs982067; hg19: chr4-19364716;