rs4131849

Variant names:

• chr4-117477239-A-G
• rs4131849
• ENST00000422145.7:n.159+48472A>G

Variant summary

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

The ENST00000422145.7(LINC01378):​n.159+48472A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.312 in 151,732 control chromosomes in the GnomAD database, including 8,439 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 0.31 (8439 hom., cov: 32)
• Consequence: LINC01378 ENST00000422145.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.572
• 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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.484 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01378	NR_125757.1	n.157+48472A>G		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01378	ENST00000422145.7	n.159+48472A>G		intron_variant	Intron 2 of 3	3
LINC01378	ENST00000437514.2	n.347+9006A>G		intron_variant	Intron 4 of 4	3
LINC01378	ENST00000626258.2	n.200+70874A>G		intron_variant	Intron 1 of 3	5

Frequencies

GnomAD3 genomes AF: 0.312 AC: 47353 AN: 151614 Hom.: 8422 Cov.: 32

Gnomad AFR AF: 0.489

Gnomad AMI AF: 0.330

Gnomad AMR AF: 0.246

Gnomad ASJ AF: 0.211

Gnomad EAS AF: 0.0762

Gnomad SAS AF: 0.198

Gnomad FIN AF: 0.240

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.263

Gnomad OTH AF: 0.273

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

GnomAD4 genome AF: 0.312 AC: 47414 AN: 151732 Hom.: 8439 Cov.: 32 AF XY: 0.306 AC XY: 22719 AN XY: 74196

African (AFR) AF: 0.489 AC: 20260 AN: 41402

American (AMR) AF: 0.246 AC: 3740 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.211 AC: 732 AN: 3464

East Asian (EAS) AF: 0.0759 AC: 394 AN: 5188

South Asian (SAS) AF: 0.199 AC: 959 AN: 4826

European-Finnish (FIN) AF: 0.240 AC: 2538 AN: 10578

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.263 AC: 17844 AN: 67732

Other (OTH) AF: 0.270 AC: 568 AN: 2106

Alfa AF: 0.302 Hom.: 1347

Bravo AF: 0.321

Asia WGS AF: 0.144 AC: 503 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.6
DANN	Benign	0.79
PhyloP100		0.57

Splicing

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

Other links and lift over

dbSNP: rs4131849; hg19: chr4-118398394;