rs11870477

chr17-69806211-A-Cchr17-69806211-A-G

Variant summary

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

The NR_109971.1(LINC01483):n.317-39229A>C 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 0.115 in 152,284 control chromosomes in the GnomAD database, including 1,393 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 0.11 (1393 hom., cov: 33)
• Consequence: LINC01483 NR_109971.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.121

Genes affected

LINC01483 (HGNC:51130): (long intergenic non-protein coding RNA 1483)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.282 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01483	NR_109971.1	n.317-39229A>C		intron_variant, non_coding_transcript_variant
LINC01483	NR_109972.1	n.317-39229A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01483	ENST00000591334.5	n.317-39229A>C		intron_variant, non_coding_transcript_variant		4
LINC01483	ENST00000587241.1	n.306+42229A>C		intron_variant, non_coding_transcript_variant		4
LINC01483	ENST00000588185.1	n.159-39229A>C		intron_variant, non_coding_transcript_variant		3
LINC01483	ENST00000665875.1	n.129+16723A>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.115 AC: 17467 AN: 152166 Hom.: 1387 Cov.: 33

Gnomad AFR AF: 0.0281

Gnomad AMI AF: 0.0877

Gnomad AMR AF: 0.190

Gnomad ASJ AF: 0.0605

Gnomad EAS AF: 0.295

Gnomad SAS AF: 0.177

Gnomad FIN AF: 0.148

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.131

Gnomad OTH AF: 0.117

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

GnomAD4 genome AF: 0.115 AC: 17482 AN: 152284 Hom.: 1393 Cov.: 33 AF XY: 0.118 AC XY: 8781 AN XY: 74458

Gnomad4 AFR AF: 0.0281

Gnomad4 AMR AF: 0.190

Gnomad4 ASJ AF: 0.0605

Gnomad4 EAS AF: 0.295

Gnomad4 SAS AF: 0.178

Gnomad4 FIN AF: 0.148

Gnomad4 NFE AF: 0.131

Gnomad4 OTH AF: 0.117

Alfa AF: 0.129 Hom.: 2869

Bravo AF: 0.115

Asia WGS AF: 0.227 AC: 792 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	1.5
Dann	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11870477; hg19: chr17-67802352;