ENST00000528720.5:n.370-4057T>C

Variant names:

• chr11-41831114-T-C
• rs1484948
• ENST00000528720.5:n.370-4057T>C

Variant summary

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

The ENST00000528720.5(LINC01499):​n.370-4057T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.236 in 152,130 control chromosomes in the GnomAD database, including 4,429 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 0.24 (4429 hom., cov: 32)
• Consequence: LINC01499 ENST00000528720.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0100
• Publications: 10 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=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.272 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01499	NR_120584.1	n.370-4057T>C		intron_variant	Intron 4 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01499	ENST00000528720.5	n.370-4057T>C		intron_variant	Intron 4 of 5	4
LINC01499	ENST00000648000.1	n.904+4871T>C		intron_variant	Intron 9 of 14
LINC01499	ENST00000824245.1	n.148-19003T>C		intron_variant	Intron 2 of 8

Frequencies

GnomAD3 genomes AF: 0.237 AC: 35961 AN: 152010 Hom.: 4428 Cov.: 32

Gnomad AFR AF: 0.210

Gnomad AMI AF: 0.295

Gnomad AMR AF: 0.216

Gnomad ASJ AF: 0.352

Gnomad EAS AF: 0.109

Gnomad SAS AF: 0.284

Gnomad FIN AF: 0.171

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.266

Gnomad OTH AF: 0.253

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

GnomAD4 genome AF: 0.236 AC: 35957 AN: 152130 Hom.: 4429 Cov.: 32 AF XY: 0.231 AC XY: 17208 AN XY: 74372

African (AFR) AF: 0.209 AC: 8693 AN: 41512

American (AMR) AF: 0.217 AC: 3306 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.352 AC: 1223 AN: 3470

East Asian (EAS) AF: 0.109 AC: 563 AN: 5164

South Asian (SAS) AF: 0.284 AC: 1372 AN: 4824

European-Finnish (FIN) AF: 0.171 AC: 1818 AN: 10602

Middle Eastern (MID) AF: 0.303 AC: 89 AN: 294

European-Non Finnish (NFE) AF: 0.266 AC: 18096 AN: 67970

Other (OTH) AF: 0.250 AC: 528 AN: 2114

Alfa AF: 0.264 Hom.: 11514

Bravo AF: 0.239

Asia WGS AF: 0.189 AC: 663 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.7
DANN	Benign	0.52
PhyloP100		-0.010

Splicing

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

Other links and lift over

dbSNP: rs1484948; hg19: chr11-41852664;