ENST00000658247.1:n.363+40469A>C

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.380 AC: 15756 AN: 41428

American (AMR) AF: 0.614 AC: 9375 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.565 AC: 1959 AN: 3470

East Asian (EAS) AF: 0.896 AC: 4631 AN: 5166

South Asian (SAS) AF: 0.516 AC: 2481 AN: 4810

European-Finnish (FIN) AF: 0.559 AC: 5909 AN: 10570

Middle Eastern (MID) AF: 0.653 AC: 192 AN: 294

European-Non Finnish (NFE) AF: 0.553 AC: 37586 AN: 67930

Other (OTH) AF: 0.578 AC: 1219 AN: 2110

Alfa AF: 0.534 Hom.: 13364

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
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs4886286; hg19: chr13-61465129;