rs1484960

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376639	XR_931213.4	n.470-1145G>C		intron_variant	Intron 4 of 6
LOC105376639	XR_931214.3	n.466-1145G>C		intron_variant	Intron 4 of 6
LOC105376639	XR_931215.3	n.298-1145G>C		intron_variant	Intron 3 of 5
LOC105376639	XR_931216.3	n.469+1159G>C		intron_variant	Intron 4 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01499	ENST00000526179.1	n.209+2063C>G		intron_variant	Intron 1 of 1	3
LINC01499	ENST00000532199.1	n.365+2063C>G		intron_variant	Intron 2 of 2	2
LINC01499	ENST00000718493.1	n.1177+1358C>G		intron_variant	Intron 6 of 8

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 v4.3

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;