4-110789885-T-C

Variant names:

• chr4-110789885-T-C
• rs4611994
• ENST00000754041.1:n.216-3544T>C

Variant summary

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

The ENST00000754041.1(LINC01438):​n.216-3544T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.192 in 151,994 control chromosomes in the GnomAD database, including 3,440 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 0.19 (3440 hom., cov: 32)
• Consequence: LINC01438 ENST00000754041.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.358
• Publications: 12 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=-0.92).
• 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

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.216-3544T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.192 AC: 29166 AN: 151876 Hom.: 3432 Cov.: 32

Gnomad AFR AF: 0.246

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.233

Gnomad ASJ AF: 0.305

Gnomad EAS AF: 0.502

Gnomad SAS AF: 0.135

Gnomad FIN AF: 0.152

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.133

Gnomad OTH AF: 0.188

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

GnomAD4 genome AF: 0.192 AC: 29206 AN: 151994 Hom.: 3440 Cov.: 32 AF XY: 0.199 AC XY: 14820 AN XY: 74324

African (AFR) AF: 0.246 AC: 10210 AN: 41426

American (AMR) AF: 0.233 AC: 3555 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.305 AC: 1057 AN: 3470

East Asian (EAS) AF: 0.503 AC: 2585 AN: 5138

South Asian (SAS) AF: 0.135 AC: 650 AN: 4822

European-Finnish (FIN) AF: 0.152 AC: 1614 AN: 10590

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.133 AC: 9057 AN: 67974

Other (OTH) AF: 0.190 AC: 400 AN: 2108

Alfa AF: 0.209 Hom.: 1379

Bravo AF: 0.202

Asia WGS AF: 0.262 AC: 911 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.3
DANN	Benign	0.56
PhyloP100		-0.36

Splicing

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

Other links and lift over

dbSNP: rs4611994; hg19: chr4-111711041;