rs1489550

Positions:

• chr4-117604999-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.158-49808A>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 0.17 in 151,936 control chromosomes in the GnomAD database, including 2,866 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 0.17 (2866 hom., cov: 32)
• Consequence: LINC01378 NR_125757.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.698

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=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.306 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC01378	NR_125757.1	n.158-49808A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01378	ENST00000626258.2	n.316+1341A>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.170 AC: 25869 AN: 151820 Hom.: 2860 Cov.: 32

Gnomad AFR AF: 0.310

Gnomad AMI AF: 0.0417

Gnomad AMR AF: 0.120

Gnomad ASJ AF: 0.226

Gnomad EAS AF: 0.145

Gnomad SAS AF: 0.0858

Gnomad FIN AF: 0.0655

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.119

Gnomad OTH AF: 0.191

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

GnomAD4 genome AF: 0.170 AC: 25902 AN: 151936 Hom.: 2866 Cov.: 32 AF XY: 0.167 AC XY: 12389 AN XY: 74250

Gnomad4 AFR AF: 0.310

Gnomad4 AMR AF: 0.120

Gnomad4 ASJ AF: 0.226

Gnomad4 EAS AF: 0.144

Gnomad4 SAS AF: 0.0856

Gnomad4 FIN AF: 0.0655

Gnomad4 NFE AF: 0.119

Gnomad4 OTH AF: 0.191

Alfa AF: 0.131 Hom.: 761

Bravo AF: 0.184

Asia WGS AF: 0.125 AC: 435 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.30
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1489550; hg19: chr4-118526154;