chr17-69806889-C-A

Position:

• chr17-69806889-C-A

Variant summary

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

The NR_109971.1(LINC01483):​n.317-38551C>A 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 152,080 control chromosomes in the GnomAD database, including 1,297 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 (1297 hom., cov: 33)
• Consequence: LINC01483 NR_109971.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.808

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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.213 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC01483	NR_109971.1	n.317-38551C>A		intron_variant, non_coding_transcript_variant
LINC01483	NR_109972.1	n.317-38551C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01483	ENST00000591334.5	n.317-38551C>A		intron_variant, non_coding_transcript_variant		4
LINC01483	ENST00000587241.1	n.306+42907C>A		intron_variant, non_coding_transcript_variant		4
LINC01483	ENST00000588185.1	n.159-38551C>A		intron_variant, non_coding_transcript_variant		3
LINC01483	ENST00000665875.1	n.129+17401C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.121 AC: 18458 AN: 151958 Hom.: 1282 Cov.: 33

Gnomad AFR AF: 0.151

Gnomad AMI AF: 0.0439

Gnomad AMR AF: 0.154

Gnomad ASJ AF: 0.109

Gnomad EAS AF: 0.223

Gnomad SAS AF: 0.105

Gnomad FIN AF: 0.132

Gnomad MID AF: 0.124

Gnomad NFE AF: 0.0899

Gnomad OTH AF: 0.108

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

GnomAD4 genome AF: 0.122 AC: 18496 AN: 152080 Hom.: 1297 Cov.: 33 AF XY: 0.126 AC XY: 9382 AN XY: 74348

Gnomad4 AFR AF: 0.152

Gnomad4 AMR AF: 0.155

Gnomad4 ASJ AF: 0.109

Gnomad4 EAS AF: 0.224

Gnomad4 SAS AF: 0.104

Gnomad4 FIN AF: 0.132

Gnomad4 NFE AF: 0.0899

Gnomad4 OTH AF: 0.106

Alfa AF: 0.109 Hom.: 123

Bravo AF: 0.126

Asia WGS AF: 0.158 AC: 546 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.63
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8072462; hg19: chr17-67803030;