rs1906591

Variant names:

• chr4-110787733-G-A
• rs1906591
• ENST00000754041.1:n.215+4010G>A

Variant summary

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

The ENST00000754041.1(LINC01438):​n.215+4010G>A 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 152,064 control chromosomes in the GnomAD database, including 2,442 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 (2442 hom., cov: 32)
• Consequence: LINC01438 ENST00000754041.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.711
• Publications: 13 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=-0.84).
• 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+4010G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.154 AC: 23461 AN: 151946 Hom.: 2437 Cov.: 32

Gnomad AFR AF: 0.115

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.220

Gnomad ASJ AF: 0.303

Gnomad EAS AF: 0.502

Gnomad SAS AF: 0.129

Gnomad FIN AF: 0.153

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.133

Gnomad OTH AF: 0.162

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

GnomAD4 genome AF: 0.154 AC: 23478 AN: 152064 Hom.: 2442 Cov.: 32 AF XY: 0.162 AC XY: 12062 AN XY: 74328

African (AFR) AF: 0.115 AC: 4787 AN: 41510

American (AMR) AF: 0.220 AC: 3353 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.303 AC: 1051 AN: 3468

East Asian (EAS) AF: 0.503 AC: 2601 AN: 5170

South Asian (SAS) AF: 0.129 AC: 623 AN: 4830

European-Finnish (FIN) AF: 0.153 AC: 1616 AN: 10556

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

European-Non Finnish (NFE) AF: 0.133 AC: 9028 AN: 67954

Other (OTH) AF: 0.163 AC: 343 AN: 2110

Alfa AF: 0.158 Hom.: 725

Bravo AF: 0.158

Asia WGS AF: 0.235 AC: 815 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	8.3
DANN	Benign	0.43
PhyloP100		0.71

Splicing

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

Other links and lift over

dbSNP: rs1906591; hg19: chr4-111708889;