13-60887877-T-C

Variant names:

• chr13-60887877-T-C
• rs300310
• ENST00000658247.1:n.363+37351T>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+37351T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.89 in 151,824 control chromosomes in the GnomAD database, including 60,220 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 0.89 (60220 hom., cov: 30)
• Consequence: LINC00378 ENST00000658247.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.73
• Publications: 3 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 = 0.976 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+37351T>C		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.891 AC: 135097 AN: 151706 Hom.: 60180 Cov.: 30

Gnomad AFR AF: 0.857

Gnomad AMI AF: 0.869

Gnomad AMR AF: 0.930

Gnomad ASJ AF: 0.935

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.901

Gnomad FIN AF: 0.903

Gnomad MID AF: 0.908

Gnomad NFE AF: 0.889

Gnomad OTH AF: 0.910

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

GnomAD4 genome AF: 0.890 AC: 135195 AN: 151824 Hom.: 60220 Cov.: 30 AF XY: 0.892 AC XY: 66157 AN XY: 74206

African (AFR) AF: 0.857 AC: 35497 AN: 41436

American (AMR) AF: 0.930 AC: 14179 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.935 AC: 3241 AN: 3468

East Asian (EAS) AF: 0.999 AC: 5034 AN: 5038

South Asian (SAS) AF: 0.901 AC: 4345 AN: 4822

European-Finnish (FIN) AF: 0.903 AC: 9549 AN: 10572

Middle Eastern (MID) AF: 0.908 AC: 267 AN: 294

European-Non Finnish (NFE) AF: 0.889 AC: 60370 AN: 67936

Other (OTH) AF: 0.912 AC: 1922 AN: 2108

Alfa AF: 0.892 Hom.: 100403

Bravo AF: 0.893

Asia WGS AF: 0.951 AC: 3304 AN: 3478

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	0.71
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs300310; hg19: chr13-61462011;