4-110793733-C-T

Variant names:

• chr4-110793733-C-T
• rs2220427
• ENST00000754041.1:n.309+211C>T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000754041.1(LINC01438):​n.309+211C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.154 in 151,974 control chromosomes in the GnomAD database, including 2,438 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 0.15 (2438 hom., cov: 31)
• Consequence: LINC01438 ENST00000754041.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.43
• Publications: 16 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.34).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.486 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.309+211C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.154 AC: 23421 AN: 151856 Hom.: 2433 Cov.: 31

Gnomad AFR AF: 0.115

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.221

Gnomad ASJ AF: 0.302

Gnomad EAS AF: 0.501

Gnomad SAS AF: 0.130

Gnomad FIN AF: 0.153

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.133

Gnomad OTH AF: 0.160

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

GnomAD4 genome AF: 0.154 AC: 23438 AN: 151974 Hom.: 2438 Cov.: 31 AF XY: 0.162 AC XY: 12046 AN XY: 74288

African (AFR) AF: 0.115 AC: 4752 AN: 41482

American (AMR) AF: 0.222 AC: 3380 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.302 AC: 1048 AN: 3468

East Asian (EAS) AF: 0.503 AC: 2577 AN: 5128

South Asian (SAS) AF: 0.129 AC: 621 AN: 4814

European-Finnish (FIN) AF: 0.153 AC: 1613 AN: 10560

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.133 AC: 9033 AN: 67960

Other (OTH) AF: 0.161 AC: 338 AN: 2104

Alfa AF: 0.133 Hom.: 4738

Bravo AF: 0.158

Asia WGS AF: 0.233 AC: 811 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.34
CADD	Benign	18
DANN	Benign	0.85
PhyloP100		1.4

Splicing

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

Other links and lift over

dbSNP: rs2220427; hg19: chr4-111714889;