chr4-178004870-T-C

Variant names:

• chr4-178004870-T-C
• rs1585576
• ENST00000667514.1:n.123-23610T>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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01098	ENST00000667514.1	n.123-23610T>C		intron_variant	Intron 1 of 1

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;