chr13-60878379-G-C

Position:

• chr13-60878379-G-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, non coding transcript 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, non_coding_transcript
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00378	ENST00000658247.1	n.363+27853G>C		intron_variant, non_coding_transcript_variant

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;