ENST00000658247.1:n.461-40944G>A

Variant names:

• chr13-61135585-G-A
• rs1514551
• ENST00000658247.1:n.461-40944G>A

Variant summary

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

The ENST00000658247.1(LINC00378):​n.461-40944G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0321 in 152,122 control chromosomes in the GnomAD database, including 220 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 0.032 (220 hom., cov: 32)
• Consequence: LINC00378 ENST00000658247.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.470

Genes affected

LINC00378 (HGNC:42704): (long intergenic non-protein coding RNA 378)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.192 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
LINC00378	ENST00000658247.1	n.461-40944G>A		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.0320 AC: 4867 AN: 152004 Hom.: 217 Cov.: 32

Gnomad AFR AF: 0.00918

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0786

Gnomad ASJ AF: 0.0170

Gnomad EAS AF: 0.202

Gnomad SAS AF: 0.0193

Gnomad FIN AF: 0.0519

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0218

Gnomad OTH AF: 0.0316

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

GnomAD4 genome AF: 0.0321 AC: 4882 AN: 152122 Hom.: 220 Cov.: 32 AF XY: 0.0349 AC XY: 2599 AN XY: 74380

Gnomad4 AFR AF: 0.00925

Gnomad4 AMR AF: 0.0794

Gnomad4 ASJ AF: 0.0170

Gnomad4 EAS AF: 0.202

Gnomad4 SAS AF: 0.0189

Gnomad4 FIN AF: 0.0519

Gnomad4 NFE AF: 0.0218

Gnomad4 OTH AF: 0.0327

Alfa AF: 0.0234 Hom.: 172

Bravo AF: 0.0366

Asia WGS AF: 0.0980 AC: 341 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	0.47
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1514551; hg19: chr13-61709719;