rs4501289

Variant names:

• chr4-117401335-G-A
• rs4501289
• ENST00000656637.1:n.372-9178G>A

Variant summary

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

The ENST00000656637.1(LINC01378):​n.372-9178G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.125 in 152,154 control chromosomes in the GnomAD database, including 1,285 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 0.12 (1285 hom., cov: 32)
• Consequence: LINC01378 ENST00000656637.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365
• Publications: 2 publications found

Genes affected

LINC01378 (HGNC:50645): (long intergenic non-protein coding RNA 1378)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.148 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
LINC01378	ENST00000656637.1	n.372-9178G>A		intron_variant	Intron 3 of 3
LINC01378	ENST00000658771.2	n.466-2732G>A		intron_variant	Intron 3 of 3
LINC01378	ENST00000717503.1	n.332+14446G>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.125 AC: 18936 AN: 152036 Hom.: 1284 Cov.: 32

Gnomad AFR AF: 0.151

Gnomad AMI AF: 0.0485

Gnomad AMR AF: 0.0863

Gnomad ASJ AF: 0.124

Gnomad EAS AF: 0.0179

Gnomad SAS AF: 0.0793

Gnomad FIN AF: 0.130

Gnomad MID AF: 0.137

Gnomad NFE AF: 0.129

Gnomad OTH AF: 0.126

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

GnomAD4 genome AF: 0.125 AC: 18947 AN: 152154 Hom.: 1285 Cov.: 32 AF XY: 0.121 AC XY: 9035 AN XY: 74380

African (AFR) AF: 0.151 AC: 6254 AN: 41508

American (AMR) AF: 0.0862 AC: 1318 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.124 AC: 430 AN: 3472

East Asian (EAS) AF: 0.0180 AC: 93 AN: 5170

South Asian (SAS) AF: 0.0791 AC: 382 AN: 4828

European-Finnish (FIN) AF: 0.130 AC: 1376 AN: 10604

Middle Eastern (MID) AF: 0.134 AC: 39 AN: 292

European-Non Finnish (NFE) AF: 0.129 AC: 8748 AN: 67980

Other (OTH) AF: 0.125 AC: 263 AN: 2108

Alfa AF: 0.128 Hom.: 483

Bravo AF: 0.123

Asia WGS AF: 0.0560 AC: 197 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.8
DANN	Benign	0.64
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs4501289; hg19: chr4-118322491;