rs8072462

Variant names:

• chr17-69806889-C-A
• rs8072462
• ENST00000587241.1:n.306+42907C>A

Variant summary

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

The ENST00000587241.1(LINC01483):​n.306+42907C>A variant causes a intron 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 ENST00000587241.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.808
• Publications: 2 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LINC01483	NR_109971.1	n.317-38551C>A		intron_variant	Intron 3 of 5
LINC01483	NR_109972.1	n.317-38551C>A		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01483	ENST00000587241.1	n.306+42907C>A		intron_variant	Intron 1 of 1	4
LINC01483	ENST00000588185.2	n.320-38551C>A		intron_variant	Intron 3 of 4	3
LINC01483	ENST00000588501.6	n.414-38551C>A		intron_variant	Intron 4 of 6	5

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

African (AFR) AF: 0.152 AC: 6282 AN: 41456

American (AMR) AF: 0.155 AC: 2362 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.109 AC: 380 AN: 3472

East Asian (EAS) AF: 0.224 AC: 1160 AN: 5174

South Asian (SAS) AF: 0.104 AC: 502 AN: 4824

European-Finnish (FIN) AF: 0.132 AC: 1398 AN: 10564

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.0899 AC: 6113 AN: 67994

Other (OTH) AF: 0.106 AC: 223 AN: 2112

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
PhyloP100		-0.81

Splicing

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

Other links and lift over

dbSNP: rs8072462; hg19: chr17-67803030;