17-69806211-A-C

Variant names:

• chr17-69806211-A-C
• rs11870477
• ENST00000587241.1:n.306+42229A>C

Variant summary

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

The ENST00000587241.1(LINC01483):​n.306+42229A>C variant causes a intron 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 ENST00000587241.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.121
• Publications: 13 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=-0.89).
• 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 rank	MANE	Protein	UniProt
LINC01483	NR_109971.1	n.317-39229A>C		intron_variant	Intron 3 of 5
LINC01483	NR_109972.1	n.317-39229A>C		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01483	ENST00000587241.1	n.306+42229A>C		intron_variant	Intron 1 of 1	4
LINC01483	ENST00000588185.2	n.320-39229A>C		intron_variant	Intron 3 of 4	3
LINC01483	ENST00000588501.6	n.414-39229A>C		intron_variant	Intron 4 of 6	5

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

African (AFR) AF: 0.0281 AC: 1167 AN: 41580

American (AMR) AF: 0.190 AC: 2911 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0605 AC: 210 AN: 3472

East Asian (EAS) AF: 0.295 AC: 1527 AN: 5180

South Asian (SAS) AF: 0.178 AC: 859 AN: 4824

European-Finnish (FIN) AF: 0.148 AC: 1569 AN: 10592

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.131 AC: 8896 AN: 68018

Other (OTH) AF: 0.117 AC: 248 AN: 2114

Alfa AF: 0.126 Hom.: 4724

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
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs11870477; hg19: chr17-67802352;