4-178004870-T-C

Position:

• chr4-178004870-T-C

Variant summary

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

The ENST00000667514.1(LINC01098):​n.123-23610T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.245 in 152,014 control chromosomes in the GnomAD database, including 5,621 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 0.25 (5621 hom., cov: 32)
• Consequence: LINC01098 ENST00000667514.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.292

Genes affected

LINC01098 (HGNC:27731): (long intergenic non-protein coding RNA 1098)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.419 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01098	ENST00000667514.1	n.123-23610T>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.245 AC: 37289 AN: 151896 Hom.: 5615 Cov.: 32

Gnomad AFR AF: 0.0815

Gnomad AMI AF: 0.300

Gnomad AMR AF: 0.428

Gnomad ASJ AF: 0.316

Gnomad EAS AF: 0.343

Gnomad SAS AF: 0.224

Gnomad FIN AF: 0.282

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.288

Gnomad OTH AF: 0.275

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

GnomAD4 genome AF: 0.245 AC: 37298 AN: 152014 Hom.: 5621 Cov.: 32 AF XY: 0.250 AC XY: 18554 AN XY: 74300

Gnomad4 AFR AF: 0.0813

Gnomad4 AMR AF: 0.428

Gnomad4 ASJ AF: 0.316

Gnomad4 EAS AF: 0.343

Gnomad4 SAS AF: 0.226

Gnomad4 FIN AF: 0.282

Gnomad4 NFE AF: 0.288

Gnomad4 OTH AF: 0.274

Alfa AF: 0.268 Hom.: 2988

Bravo AF: 0.257

Asia WGS AF: 0.260 AC: 907 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	8.5
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: rs1585576; hg19: chr4-178926024;