13-60878379-G-C

Variant names:

• chr13-60878379-G-C
• rs301653
• ENST00000658247.1:n.363+27853G>C

Variant summary

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

The ENST00000658247.1(LINC00378):​n.363+27853G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.876 in 152,174 control chromosomes in the GnomAD database, including 58,448 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 0.88 (58448 hom., cov: 32)
• Consequence: LINC00378 ENST00000658247.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.328

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 = 0.976 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.363+27853G>C		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.876 AC: 133183 AN: 152056 Hom.: 58405 Cov.: 32

Gnomad AFR AF: 0.857

Gnomad AMI AF: 0.866

Gnomad AMR AF: 0.909

Gnomad ASJ AF: 0.909

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.896

Gnomad FIN AF: 0.901

Gnomad MID AF: 0.854

Gnomad NFE AF: 0.863

Gnomad OTH AF: 0.881

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

GnomAD4 genome AF: 0.876 AC: 133281 AN: 152174 Hom.: 58448 Cov.: 32 AF XY: 0.879 AC XY: 65357 AN XY: 74388

Gnomad4 AFR AF: 0.857

Gnomad4 AMR AF: 0.910

Gnomad4 ASJ AF: 0.909

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.896

Gnomad4 FIN AF: 0.901

Gnomad4 NFE AF: 0.863

Gnomad4 OTH AF: 0.883

Alfa AF: 0.844 Hom.: 2655

Bravo AF: 0.877

Asia WGS AF: 0.949 AC: 3298 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	0.92
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs301653; hg19: chr13-61452513;