rs4131849

Positions:

• chr4-117477239-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_125757.1(LINC01378):​n.157+48472A>G variant causes a intron, non coding transcript 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 NR_125757.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.572

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
LINC01378	NR_125757.1	n.157+48472A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01378	ENST00000626258.2	n.200+70874A>G		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.489

Gnomad4 AMR AF: 0.246

Gnomad4 ASJ AF: 0.211

Gnomad4 EAS AF: 0.0759

Gnomad4 SAS AF: 0.199

Gnomad4 FIN AF: 0.240

Gnomad4 NFE AF: 0.263

Gnomad4 OTH AF: 0.270

Alfa AF: 0.297 Hom.: 1264

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4131849; hg19: chr4-118398394;