ENST00000526179.1:n.209+2063C>G

Variant names:

• chr11-41858617-C-G
• rs1484960
• ENST00000526179.1:n.209+2063C>G

Variant summary

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

The ENST00000526179.1(LINC01499):​n.209+2063C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.456 in 151,836 control chromosomes in the GnomAD database, including 18,486 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 0.46 (18486 hom., cov: 32)
• Consequence: LINC01499 ENST00000526179.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.242
• Publications: 0 publications found

Genes affected

LINC01499 (HGNC:51165): (long intergenic non-protein coding RNA 1499)

ENSG00000307159 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.74 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000526179.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01499	ENST00000526179.1	TSL:3	n.209+2063C>G		intron	N/A
	LINC01499	ENST00000532199.1	TSL:2	n.365+2063C>G		intron	N/A
	LINC01499	ENST00000718493.1		n.1177+1358C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.456 AC: 69109 AN: 151718 Hom.: 18456 Cov.: 32

Gnomad AFR AF: 0.747

Gnomad AMI AF: 0.371

Gnomad AMR AF: 0.335

Gnomad ASJ AF: 0.452

Gnomad EAS AF: 0.265

Gnomad SAS AF: 0.439

Gnomad FIN AF: 0.233

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.357

Gnomad OTH AF: 0.442

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

GnomAD4 genome AF: 0.456 AC: 69178 AN: 151836 Hom.: 18486 Cov.: 32 AF XY: 0.447 AC XY: 33162 AN XY: 74196

African (AFR) AF: 0.747 AC: 30930 AN: 41424

American (AMR) AF: 0.335 AC: 5097 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.452 AC: 1569 AN: 3468

East Asian (EAS) AF: 0.264 AC: 1363 AN: 5158

South Asian (SAS) AF: 0.438 AC: 2113 AN: 4820

European-Finnish (FIN) AF: 0.233 AC: 2455 AN: 10530

Middle Eastern (MID) AF: 0.463 AC: 136 AN: 294

European-Non Finnish (NFE) AF: 0.357 AC: 24258 AN: 67892

Other (OTH) AF: 0.436 AC: 920 AN: 2108

Alfa AF: 0.408 Hom.: 1836

Bravo AF: 0.475

Asia WGS AF: 0.342 AC: 1193 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.66
DANN	Benign	0.48
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs1484960; hg19: chr11-41880167;