rs1455311

Variant names:

• chr4-79043433-A-G
• rs1455311
• ENST00000509088.7:n.468-42663A>G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000509088.7(LINC01088):​n.468-42663A>G variant causes a intron 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 ENST00000509088.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.63
• Publications: 11 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01088	NR_038342.1		n.183-42663A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01088	ENST00000509088.7	TSL:1	n.468-42663A>G		intron	N/A
	LINC01088	ENST00000510667.5	TSL:3	n.130-42663A>G		intron	N/A
	LINC01088	ENST00000651041.1		n.133-42663A>G		intron	N/A

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

African (AFR) AF: 0.0872 AC: 3618 AN: 41510

American (AMR) AF: 0.128 AC: 1955 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.198 AC: 688 AN: 3472

East Asian (EAS) AF: 0.141 AC: 730 AN: 5168

South Asian (SAS) AF: 0.112 AC: 537 AN: 4816

European-Finnish (FIN) AF: 0.152 AC: 1611 AN: 10576

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.165 AC: 11242 AN: 67946

Other (OTH) AF: 0.174 AC: 366 AN: 2108

Alfa AF: 0.228 Hom.: 16985

Bravo AF: 0.138

Asia WGS AF: 0.126 AC: 435 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.25
CADD	Benign	19
DANN	Benign	0.84
PhyloP100		4.6

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: rs1455311;

hg19: chr4-79964587;