rs4886286

Variant names:

• chr13-60890995-A-C
• rs4886286
• ENST00000658247.1:n.363+40469A>C

Your query was ambiguous. Multiple possible variants found:

• chr13-60890995-A-C
• chr13-60890995-A-G
• chr13-60890995-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 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
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00378	ENST00000658247.1	n.363+40469A>C		intron_variant	Intron 3 of 4

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;