4-110789013-C-T

Variant names:

• chr4-110789013-C-T
• rs2200733
• ENST00000754041.1:n.216-4416C>T

Variant summary

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

The ENST00000754041.1(LINC01438):​n.216-4416C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.184 in 152,078 control chromosomes in the GnomAD database, including 3,161 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 0.18 (3161 hom., cov: 32)
• Consequence: LINC01438 ENST00000754041.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.360
• Publications: 243 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.487 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

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
	LINC01438	ENST00000754041.1		n.216-4416C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.184 AC: 27975 AN: 151960 Hom.: 3155 Cov.: 32

Gnomad AFR AF: 0.220

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.229

Gnomad ASJ AF: 0.304

Gnomad EAS AF: 0.502

Gnomad SAS AF: 0.130

Gnomad FIN AF: 0.153

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.133

Gnomad OTH AF: 0.179

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

GnomAD4 genome AF: 0.184 AC: 28002 AN: 152078 Hom.: 3161 Cov.: 32 AF XY: 0.192 AC XY: 14262 AN XY: 74332

African (AFR) AF: 0.220 AC: 9113 AN: 41470

American (AMR) AF: 0.229 AC: 3495 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.304 AC: 1057 AN: 3472

East Asian (EAS) AF: 0.503 AC: 2587 AN: 5140

South Asian (SAS) AF: 0.129 AC: 624 AN: 4822

European-Finnish (FIN) AF: 0.153 AC: 1617 AN: 10580

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.133 AC: 9054 AN: 68014

Other (OTH) AF: 0.179 AC: 378 AN: 2110

Alfa AF: 0.147 Hom.: 7603

Bravo AF: 0.192

Asia WGS AF: 0.239 AC: 833 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.1
DANN	Benign	0.33
PhyloP100		-0.36

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: rs2200733;

hg19: chr4-111710169;