4-13806736-A-G

Variant names:

• chr4-13806736-A-G
• rs10489088
• ENST00000510907.5:n.282-23044A>G

Variant summary

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

The ENST00000510907.5(LINC01182):​n.282-23044A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.106 in 152,180 control chromosomes in the GnomAD database, including 1,067 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 0.11 (1067 hom., cov: 32)
• Consequence: LINC01182 ENST00000510907.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.263
• Publications: 3 publications found

Genes affected

LINC01182 (HGNC:49564): (long intergenic non-protein coding RNA 1182)

ENSG00000288951 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.166 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000510907.5. 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
	LINC01182	NR_121681.1		n.282-23044A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01182	ENST00000510907.5	TSL:2	n.282-23044A>G		intron	N/A
	LINC01182	ENST00000669061.1		n.549-23044A>G		intron	N/A
	ENSG00000288951	ENST00000689499.3		n.192+34025T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.106 AC: 16176 AN: 152062 Hom.: 1065 Cov.: 32

Gnomad AFR AF: 0.0345

Gnomad AMI AF: 0.0461

Gnomad AMR AF: 0.0771

Gnomad ASJ AF: 0.0605

Gnomad EAS AF: 0.176

Gnomad SAS AF: 0.0966

Gnomad FIN AF: 0.167

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.147

Gnomad OTH AF: 0.0937

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

GnomAD4 genome AF: 0.106 AC: 16180 AN: 152180 Hom.: 1067 Cov.: 32 AF XY: 0.108 AC XY: 8024 AN XY: 74414

African (AFR) AF: 0.0344 AC: 1429 AN: 41526

American (AMR) AF: 0.0770 AC: 1177 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0605 AC: 210 AN: 3472

East Asian (EAS) AF: 0.175 AC: 905 AN: 5164

South Asian (SAS) AF: 0.0978 AC: 471 AN: 4818

European-Finnish (FIN) AF: 0.167 AC: 1761 AN: 10576

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.147 AC: 9973 AN: 68012

Other (OTH) AF: 0.0951 AC: 201 AN: 2114

Alfa AF: 0.121 Hom.: 2182

Bravo AF: 0.0971

Asia WGS AF: 0.122 AC: 426 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.1
DANN	Benign	0.70
PhyloP100		0.26

Splicing

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

Other links and lift over

dbSNP: rs10489088; hg19: chr4-13808360;