ENST00000528720.5:n.37-5712C>T

Variant names:

• chr11-41728960-C-T
• rs1960350
• ENST00000528720.5:n.37-5712C>T

Variant summary

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

The ENST00000528720.5(LINC01499):​n.37-5712C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.226 in 152,096 control chromosomes in the GnomAD database, including 4,162 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 0.23 (4162 hom., cov: 33)
• Consequence: LINC01499 ENST00000528720.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.187
• Publications: 3 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.447 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000528720.5. 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
	LINC01499	NR_120584.1		n.37-5712C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01499	ENST00000528720.5	TSL:4	n.37-5712C>T		intron	N/A
	LINC01499	ENST00000529282.1	TSL:4	n.169-5712C>T		intron	N/A
	LINC01499	ENST00000530379.1	TSL:4	n.473-5712C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.226 AC: 34372 AN: 151978 Hom.: 4159 Cov.: 33

Gnomad AFR AF: 0.216

Gnomad AMI AF: 0.207

Gnomad AMR AF: 0.285

Gnomad ASJ AF: 0.239

Gnomad EAS AF: 0.462

Gnomad SAS AF: 0.229

Gnomad FIN AF: 0.164

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.209

Gnomad OTH AF: 0.256

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

GnomAD4 genome AF: 0.226 AC: 34411 AN: 152096 Hom.: 4162 Cov.: 33 AF XY: 0.226 AC XY: 16822 AN XY: 74360

African (AFR) AF: 0.216 AC: 8979 AN: 41512

American (AMR) AF: 0.286 AC: 4364 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.239 AC: 827 AN: 3466

East Asian (EAS) AF: 0.462 AC: 2362 AN: 5112

South Asian (SAS) AF: 0.228 AC: 1100 AN: 4830

European-Finnish (FIN) AF: 0.164 AC: 1737 AN: 10598

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.209 AC: 14233 AN: 67976

Other (OTH) AF: 0.256 AC: 542 AN: 2116

Alfa AF: 0.223 Hom.: 4830

Bravo AF: 0.241

Asia WGS AF: 0.343 AC: 1194 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	5.7
DANN	Benign	0.29
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs1960350; hg19: chr11-41750510;