rs899900

chr4-79018379-G-Cchr4-79018379-G-T

Variant summary

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

The NR_038342.1(LINC01088):n.182+45327G>C variant causes a intron, non coding transcript 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 NR_038342.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0230

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01088	NR_038342.1	n.182+45327G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01088	ENST00000658852.1	n.232+45327G>C		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.229

Gnomad4 AMR AF: 0.783

Gnomad4 ASJ AF: 0.779

Gnomad4 EAS AF: 0.948

Gnomad4 SAS AF: 0.878

Gnomad4 FIN AF: 0.802

Gnomad4 NFE AF: 0.813

Gnomad4 OTH AF: 0.692

Alfa AF: 0.609 Hom.: 2182

Bravo AF: 0.633

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	1.1
Dann	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs899900; hg19: chr4-79939533;