4-110792167-C-T

Variant names:

• chr4-110792167-C-T
• rs1906602
• ENST00000754041.1:n.216-1262C>T

Variant summary

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

The ENST00000754041.1(LINC01438):​n.216-1262C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.96 in 152,284 control chromosomes in the GnomAD database, including 70,458 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 0.96 (70458 hom., cov: 33)
• Consequence: LINC01438 ENST00000754041.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.710
• Publications: 2 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=-0.56).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.993 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01438	ENST00000754041.1		n.216-1262C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.960 AC: 146140 AN: 152166 Hom.: 70427 Cov.: 33

Gnomad AFR AF: 0.863

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.985

Gnomad ASJ AF: 0.998

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.995

Gnomad FIN AF: 1.00

Gnomad MID AF: 0.994

Gnomad NFE AF: 0.999

Gnomad OTH AF: 0.973

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

GnomAD4 genome AF: 0.960 AC: 146229 AN: 152284 Hom.: 70458 Cov.: 33 AF XY: 0.961 AC XY: 71532 AN XY: 74460

African (AFR) AF: 0.863 AC: 35854 AN: 41532

American (AMR) AF: 0.985 AC: 15053 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.998 AC: 3464 AN: 3470

East Asian (EAS) AF: 0.999 AC: 5175 AN: 5182

South Asian (SAS) AF: 0.995 AC: 4806 AN: 4832

European-Finnish (FIN) AF: 1.00 AC: 10627 AN: 10628

Middle Eastern (MID) AF: 0.993 AC: 292 AN: 294

European-Non Finnish (NFE) AF: 0.999 AC: 67992 AN: 68034

Other (OTH) AF: 0.972 AC: 2054 AN: 2114

Alfa AF: 0.992 Hom.: 92871

Bravo AF: 0.954

Asia WGS AF: 0.975 AC: 3386 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.56
CADD	Benign	9.1
DANN	Benign	0.76
PhyloP100		-0.71

Splicing

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

Other links and lift over

dbSNP: rs1906602; hg19: chr4-111713323;