rs4886286

chr13-60890995-A-Cchr13-60890995-A-Gchr13-60890995-A-T

Variant summary

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

The ENST00000658247.1(LINC00378):n.363+40469A>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 0.523 in 151,952 control chromosomes in the GnomAD database, including 21,862 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 0.52 (21862 hom., cov: 31)
• Consequence: LINC00378 ENST00000658247.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13

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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.875 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+40469A>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.524 AC: 79501 AN: 151834 Hom.: 21860 Cov.: 31

Gnomad AFR AF: 0.381

Gnomad AMI AF: 0.480

Gnomad AMR AF: 0.614

Gnomad ASJ AF: 0.565

Gnomad EAS AF: 0.896

Gnomad SAS AF: 0.515

Gnomad FIN AF: 0.559

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.553

Gnomad OTH AF: 0.576

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

GnomAD4 genome AF: 0.523 AC: 79546 AN: 151952 Hom.: 21862 Cov.: 31 AF XY: 0.525 AC XY: 38950 AN XY: 74242

Gnomad4 AFR AF: 0.380

Gnomad4 AMR AF: 0.614

Gnomad4 ASJ AF: 0.565

Gnomad4 EAS AF: 0.896

Gnomad4 SAS AF: 0.516

Gnomad4 FIN AF: 0.559

Gnomad4 NFE AF: 0.553

Gnomad4 OTH AF: 0.578

Alfa AF: 0.519 Hom.: 7898

Bravo AF: 0.527

Asia WGS AF: 0.713 AC: 2472 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	0.37
Dann	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4886286; hg19: chr13-61465129;