rs3106598

Variant names:

• chr13-61104778-G-A
• rs3106598
• ENST00000658247.1:n.461-71751G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000658247.1(LINC00378):​n.461-71751G>A variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.30
• Publications: 8 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=-0.96).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00378	ENST00000658247.1	n.461-71751G>A		intron_variant	Intron 4 of 4

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

African (AFR) AF: 0.308 AC: 12759 AN: 41488

American (AMR) AF: 0.493 AC: 7525 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.473 AC: 1641 AN: 3468

East Asian (EAS) AF: 0.555 AC: 2864 AN: 5160

South Asian (SAS) AF: 0.460 AC: 2213 AN: 4810

European-Finnish (FIN) AF: 0.505 AC: 5334 AN: 10552

Middle Eastern (MID) AF: 0.425 AC: 124 AN: 292

European-Non Finnish (NFE) AF: 0.468 AC: 31819 AN: 67952

Other (OTH) AF: 0.432 AC: 914 AN: 2116

Alfa AF: 0.454 Hom.: 57803

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
PhyloP100		-1.3

Splicing

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

Other links and lift over

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