4-178004870-T-C

Variant names:

• chr4-178004870-T-C
• rs1585576
• ENST00000667514.2:n.141-23610T>C

Variant summary

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

The ENST00000667514.2(LINC01098):​n.141-23610T>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 ENST00000667514.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.292
• Publications: 5 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000667514.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01098	ENST00000667514.2		n.141-23610T>C		intron	N/A

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

African (AFR) AF: 0.0813 AC: 3375 AN: 41536

American (AMR) AF: 0.428 AC: 6514 AN: 15214

Ashkenazi Jewish (ASJ) AF: 0.316 AC: 1096 AN: 3470

East Asian (EAS) AF: 0.343 AC: 1762 AN: 5138

South Asian (SAS) AF: 0.226 AC: 1088 AN: 4820

European-Finnish (FIN) AF: 0.282 AC: 2986 AN: 10578

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.288 AC: 19551 AN: 67950

Other (OTH) AF: 0.274 AC: 576 AN: 2106

Alfa AF: 0.275 Hom.: 4158

Bravo AF: 0.257

Asia WGS AF: 0.260 AC: 907 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	8.5
DANN	Benign	0.79
PhyloP100		0.29

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1585576;

hg19: chr4-178926024;