rs3106598

chr13-61104778-G-A

Variant summary

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

The ENST00000658247.1(LINC00378):n.461-71751G>A 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 0.432 in 152,018 control chromosomes in the GnomAD database, including 14,744 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 0.43 (14744 hom., cov: 33)
• Consequence: LINC00378 ENST00000658247.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.30

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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.538 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.461-71751G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.432 AC: 65612 AN: 151900 Hom.: 14745 Cov.: 33

Gnomad AFR AF: 0.308

Gnomad AMI AF: 0.472

Gnomad AMR AF: 0.492

Gnomad ASJ AF: 0.473

Gnomad EAS AF: 0.554

Gnomad SAS AF: 0.461

Gnomad FIN AF: 0.505

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.468

Gnomad OTH AF: 0.437

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

GnomAD4 genome AF: 0.432 AC: 65621 AN: 152018 Hom.: 14744 Cov.: 33 AF XY: 0.435 AC XY: 32311 AN XY: 74294

Gnomad4 AFR AF: 0.308

Gnomad4 AMR AF: 0.493

Gnomad4 ASJ AF: 0.473

Gnomad4 EAS AF: 0.555

Gnomad4 SAS AF: 0.460

Gnomad4 FIN AF: 0.505

Gnomad4 NFE AF: 0.468

Gnomad4 OTH AF: 0.432

Alfa AF: 0.461 Hom.: 37902

Bravo AF: 0.425

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.18
Dann	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3106598; hg19: chr13-61678912; COSMIC: COSV69356292;