rs302883

Variant names:

• chr13-60994350-A-G
• rs302883
• ENST00000658247.1:n.460+1994A>G

Variant summary

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

The ENST00000658247.1(LINC00378):​n.460+1994A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.134 in 151,848 control chromosomes in the GnomAD database, including 1,616 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 0.13 (1616 hom., cov: 31)
• Consequence: LINC00378 ENST00000658247.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.240

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 (NFE) allele frequency at 95% confidence interval = 0.179 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.460+1994A>G		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.134 AC: 20329 AN: 151730 Hom.: 1615 Cov.: 31

Gnomad AFR AF: 0.0581

Gnomad AMI AF: 0.201

Gnomad AMR AF: 0.114

Gnomad ASJ AF: 0.156

Gnomad EAS AF: 0.0559

Gnomad SAS AF: 0.133

Gnomad FIN AF: 0.182

Gnomad MID AF: 0.0924

Gnomad NFE AF: 0.182

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.134 AC: 20332 AN: 151848 Hom.: 1616 Cov.: 31 AF XY: 0.134 AC XY: 9970 AN XY: 74196

Gnomad4 AFR AF: 0.0581

Gnomad4 AMR AF: 0.114

Gnomad4 ASJ AF: 0.156

Gnomad4 EAS AF: 0.0556

Gnomad4 SAS AF: 0.133

Gnomad4 FIN AF: 0.182

Gnomad4 NFE AF: 0.182

Gnomad4 OTH AF: 0.123

Alfa AF: 0.163 Hom.: 284

Bravo AF: 0.124

Asia WGS AF: 0.0810 AC: 281 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	7.2
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs302883; hg19: chr13-61568484;