rs11658127

chr17-68718141-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000587999.1(LINC01482):n.199-45349A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.122 in 152,090 control chromosomes in the GnomAD database, including 1,173 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 (1173 hom., cov: 31)
• Consequence: LINC01482 ENST00000587999.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0950

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.218 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01482	ENST00000587999.1	n.199-45349A>G		intron_variant, non_coding_transcript_variant		3
LINC01482	ENST00000589610.5	n.129-31974A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.122 AC: 18579 AN: 151972 Hom.: 1171 Cov.: 31

Gnomad AFR AF: 0.123

Gnomad AMI AF: 0.0493

Gnomad AMR AF: 0.105

Gnomad ASJ AF: 0.161

Gnomad EAS AF: 0.228

Gnomad SAS AF: 0.167

Gnomad FIN AF: 0.0664

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.122

Gnomad OTH AF: 0.129

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

GnomAD4 genome AF: 0.122 AC: 18585 AN: 152090 Hom.: 1173 Cov.: 31 AF XY: 0.121 AC XY: 9015 AN XY: 74352

Gnomad4 AFR AF: 0.123

Gnomad4 AMR AF: 0.105

Gnomad4 ASJ AF: 0.161

Gnomad4 EAS AF: 0.229

Gnomad4 SAS AF: 0.168

Gnomad4 FIN AF: 0.0664

Gnomad4 NFE AF: 0.122

Gnomad4 OTH AF: 0.130

Alfa AF: 0.126 Hom.: 2214

Bravo AF: 0.121

Asia WGS AF: 0.203 AC: 705 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	5.4
Dann	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11658127; hg19: chr17-66714282;