4-79018379-G-C

Variant names:

• chr4-79018379-G-C
• rs899900
• ENST00000509088.7:n.467+45327G>C

Variant summary

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

The ENST00000509088.7(LINC01088):​n.467+45327G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.655 in 152,028 control chromosomes in the GnomAD database, including 38,031 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 0.65 (38031 hom., cov: 31)
• Consequence: LINC01088 ENST00000509088.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0230
• Publications: 2 publications found

Genes affected

LINC01088 (HGNC:49148): (long intergenic non-protein coding RNA 1088)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.926 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000509088.7. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01088	NR_038342.1		n.182+45327G>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01088	ENST00000509088.7	TSL:1	n.467+45327G>C		intron	N/A
	LINC01088	ENST00000510667.5	TSL:3	n.129+46503G>C		intron	N/A
	LINC01088	ENST00000651041.1		n.132+46503G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.655 AC: 99496 AN: 151910 Hom.: 38032 Cov.: 31

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.915

Gnomad AMR AF: 0.783

Gnomad ASJ AF: 0.779

Gnomad EAS AF: 0.948

Gnomad SAS AF: 0.879

Gnomad FIN AF: 0.802

Gnomad MID AF: 0.680

Gnomad NFE AF: 0.813

Gnomad OTH AF: 0.690

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

GnomAD4 genome AF: 0.655 AC: 99512 AN: 152028 Hom.: 38031 Cov.: 31 AF XY: 0.660 AC XY: 49086 AN XY: 74326

African (AFR) AF: 0.229 AC: 9474 AN: 41436

American (AMR) AF: 0.783 AC: 11965 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.779 AC: 2702 AN: 3468

East Asian (EAS) AF: 0.948 AC: 4895 AN: 5162

South Asian (SAS) AF: 0.878 AC: 4222 AN: 4810

European-Finnish (FIN) AF: 0.802 AC: 8487 AN: 10578

Middle Eastern (MID) AF: 0.697 AC: 205 AN: 294

European-Non Finnish (NFE) AF: 0.813 AC: 55267 AN: 67982

Other (OTH) AF: 0.692 AC: 1462 AN: 2114

Alfa AF: 0.609 Hom.: 2182

Bravo AF: 0.633

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.1
DANN	Benign	0.55
PhyloP100		0.023

Splicing

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

Other links and lift over

dbSNP: rs899900; hg19: chr4-79939533;