rs1484948

Positions:

• chr11-41831114-T-C

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

LINC01499 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
LINC01499	NR_120584.1	n.370-4057T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01499	ENST00000528720.5	n.370-4057T>C		intron_variant		4
LINC01499	ENST00000648000.1	n.904+4871T>C		intron_variant

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

Gnomad4 AFR AF: 0.209

Gnomad4 AMR AF: 0.217

Gnomad4 ASJ AF: 0.352

Gnomad4 EAS AF: 0.109

Gnomad4 SAS AF: 0.284

Gnomad4 FIN AF: 0.171

Gnomad4 NFE AF: 0.266

Gnomad4 OTH AF: 0.250

Alfa AF: 0.269 Hom.: 8156

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1484948; hg19: chr11-41852664;