4-19248810-C-G

Position:

• chr4-19248810-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000505347.1(LINC02438):​n.450-76284G>C variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.305

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=-0.93).
• 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/exons	MANE	UniProt
LINC02438	XR_001741605.2	n.446-29947G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02438	ENST00000505347.1	n.450-76284G>C		intron_variant, non_coding_transcript_variant		3
LINC02438	ENST00000669321.1	n.400-29947G>C		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.541

Gnomad4 AMR AF: 0.587

Gnomad4 ASJ AF: 0.493

Gnomad4 EAS AF: 0.545

Gnomad4 SAS AF: 0.451

Gnomad4 FIN AF: 0.578

Gnomad4 NFE AF: 0.444

Gnomad4 OTH AF: 0.499

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs312364; hg19: chr4-19250433;