4-110784612-T-C

Variant names:

• chr4-110784612-T-C
• rs6817105
• ENST00000754041.1:n.215+889T>C

Variant summary

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

The ENST00000754041.1(LINC01438):​n.215+889T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.19 in 152,074 control chromosomes in the GnomAD database, including 3,375 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 (3375 hom., cov: 32)
• Consequence: LINC01438 ENST00000754041.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.85
• Publications: 56 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01438	ENST00000754041.1	n.215+889T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.190 AC: 28890 AN: 151954 Hom.: 3366 Cov.: 32

Gnomad AFR AF: 0.239

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.232

Gnomad ASJ AF: 0.305

Gnomad EAS AF: 0.502

Gnomad SAS AF: 0.134

Gnomad FIN AF: 0.152

Gnomad MID AF: 0.208

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: 0.190 AC: 28931 AN: 152074 Hom.: 3375 Cov.: 32 AF XY: 0.198 AC XY: 14706 AN XY: 74392

African (AFR) AF: 0.239 AC: 9932 AN: 41486

American (AMR) AF: 0.233 AC: 3553 AN: 15272

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

East Asian (EAS) AF: 0.503 AC: 2602 AN: 5168

South Asian (SAS) AF: 0.134 AC: 647 AN: 4824

European-Finnish (FIN) AF: 0.152 AC: 1604 AN: 10556

Middle Eastern (MID) AF: 0.217 AC: 63 AN: 290

European-Non Finnish (NFE) AF: 0.133 AC: 9060 AN: 67984

Other (OTH) AF: 0.189 AC: 400 AN: 2112

Alfa AF: 0.140 Hom.: 4538

Bravo AF: 0.200

Asia WGS AF: 0.261 AC: 903 AN: 3456

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.0090
DANN	Benign	0.53
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs6817105; hg19: chr4-111705768;