rs11658297

Variant names:

• chr17-68732842-G-A
• rs11658297
• ENST00000587999.1:n.199-30648G>A

Variant summary

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

The ENST00000587999.1(LINC01482):​n.199-30648G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.116 in 152,150 control chromosomes in the GnomAD database, including 1,069 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 0.12 (1069 hom., cov: 32)
• Consequence: LINC01482 ENST00000587999.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.54
• Publications: 6 publications found

Genes affected

LINC01482 (HGNC:51128): (long intergenic non-protein coding RNA 1482)

ENSG00000303167 (HGNC:):

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 = 0.219 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01482	ENST00000587999.1	n.199-30648G>A		intron_variant	Intron 2 of 2	3
LINC01482	ENST00000589610.5	n.129-17273G>A		intron_variant	Intron 2 of 3	3
LINC01482	ENST00000792224.1	n.142-17273G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.116 AC: 17641 AN: 152032 Hom.: 1068 Cov.: 32

Gnomad AFR AF: 0.0990

Gnomad AMI AF: 0.142

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.161

Gnomad EAS AF: 0.229

Gnomad SAS AF: 0.168

Gnomad FIN AF: 0.0661

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.122

Gnomad OTH AF: 0.124

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

GnomAD4 genome AF: 0.116 AC: 17645 AN: 152150 Hom.: 1069 Cov.: 32 AF XY: 0.115 AC XY: 8585 AN XY: 74396

African (AFR) AF: 0.0988 AC: 4100 AN: 41496

American (AMR) AF: 0.104 AC: 1587 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.161 AC: 557 AN: 3468

East Asian (EAS) AF: 0.229 AC: 1188 AN: 5178

South Asian (SAS) AF: 0.169 AC: 812 AN: 4816

European-Finnish (FIN) AF: 0.0661 AC: 700 AN: 10588

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.122 AC: 8275 AN: 68004

Other (OTH) AF: 0.125 AC: 264 AN: 2116

Alfa AF: 0.120 Hom.: 1829

Bravo AF: 0.114

Asia WGS AF: 0.207 AC: 719 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.13
DANN	Benign	0.57
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs11658297; hg19: chr17-66728983;