rs1455311

chr4-79043433-A-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NR_038342.1(LINC01088):n.183-42663A>G variant causes a intron, non coding transcript change. The variant allele was found at a frequency of 0.139 in 152,088 control chromosomes in the GnomAD database, including 1,588 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 0.14 (1588 hom., cov: 32)
• Consequence: LINC01088 NR_038342.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.63

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.25).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.163 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01088	NR_038342.1	n.183-42663A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01088	ENST00000658852.1	n.233-42663A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.139 AC: 21070 AN: 151970 Hom.: 1587 Cov.: 32

Gnomad AFR AF: 0.0872

Gnomad AMI AF: 0.288

Gnomad AMR AF: 0.128

Gnomad ASJ AF: 0.198

Gnomad EAS AF: 0.141

Gnomad SAS AF: 0.112

Gnomad FIN AF: 0.152

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.165

Gnomad OTH AF: 0.171

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

GnomAD4 genome AF: 0.139 AC: 21076 AN: 152088 Hom.: 1588 Cov.: 32 AF XY: 0.138 AC XY: 10299 AN XY: 74362

Gnomad4 AFR AF: 0.0872

Gnomad4 AMR AF: 0.128

Gnomad4 ASJ AF: 0.198

Gnomad4 EAS AF: 0.141

Gnomad4 SAS AF: 0.112

Gnomad4 FIN AF: 0.152

Gnomad4 NFE AF: 0.165

Gnomad4 OTH AF: 0.174

Alfa AF: 0.241 Hom.: 11955

Bravo AF: 0.138

Asia WGS AF: 0.126 AC: 435 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.25
Cadd	Benign	19
Dann	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1455311; hg19: chr4-79964587;