4-110793263-T-G

Variant names:

• chr4-110793263-T-G
• rs13143308
• ENST00000754041.1:n.216-166T>G

Variant summary

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

The ENST00000754041.1(LINC01438):​n.216-166T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.704 in 151,978 control chromosomes in the GnomAD database, including 38,555 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 0.70 (38555 hom., cov: 32)
• Consequence: LINC01438 ENST00000754041.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.78
• Publications: 21 publications found

Genes affected

LINC01438 (HGNC:50757): (long intergenic non-protein coding RNA 1438)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.765 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000754041.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01438	ENST00000754041.1		n.216-166T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.704 AC: 106892 AN: 151858 Hom.: 38527 Cov.: 32

Gnomad AFR AF: 0.702

Gnomad AMI AF: 0.922

Gnomad AMR AF: 0.593

Gnomad ASJ AF: 0.622

Gnomad EAS AF: 0.270

Gnomad SAS AF: 0.660

Gnomad FIN AF: 0.679

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.771

Gnomad OTH AF: 0.708

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

GnomAD4 genome AF: 0.704 AC: 106968 AN: 151978 Hom.: 38555 Cov.: 32 AF XY: 0.688 AC XY: 51116 AN XY: 74274

African (AFR) AF: 0.702 AC: 29115 AN: 41448

American (AMR) AF: 0.593 AC: 9043 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.622 AC: 2161 AN: 3472

East Asian (EAS) AF: 0.270 AC: 1391 AN: 5156

South Asian (SAS) AF: 0.660 AC: 3177 AN: 4812

European-Finnish (FIN) AF: 0.679 AC: 7165 AN: 10558

Middle Eastern (MID) AF: 0.697 AC: 205 AN: 294

European-Non Finnish (NFE) AF: 0.771 AC: 52381 AN: 67966

Other (OTH) AF: 0.706 AC: 1489 AN: 2108

Alfa AF: 0.758 Hom.: 101601

Bravo AF: 0.700

Asia WGS AF: 0.501 AC: 1744 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	0.32
DANN	Benign	0.80
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs13143308; hg19: chr4-111714419;