rs558473

Variant names:

• chr4-13982691-A-G
• rs558473
• ENST00000657663.1:n.136-18130A>G

Variant summary

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

The ENST00000657663.1(LINC01182):​n.136-18130A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.476 in 151,324 control chromosomes in the GnomAD database, including 17,551 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 0.48 (17551 hom., cov: 29)
• Consequence: LINC01182 ENST00000657663.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.629
• Publications: 0 publications found

Genes affected

LINC01182 (HGNC:49564): (long intergenic non-protein coding RNA 1182)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.565 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01182	ENST00000657663.1	n.136-18130A>G		intron_variant	Intron 1 of 1
LINC01182	ENST00000669061.1	n.714-18130A>G		intron_variant	Intron 4 of 4
LINC01182	ENST00000715489.1	n.727+49346A>G		intron_variant	Intron 5 of 8

Frequencies

GnomAD3 genomes AF: 0.476 AC: 72027 AN: 151206 Hom.: 17545 Cov.: 29

Gnomad AFR AF: 0.572

Gnomad AMI AF: 0.378

Gnomad AMR AF: 0.454

Gnomad ASJ AF: 0.538

Gnomad EAS AF: 0.305

Gnomad SAS AF: 0.538

Gnomad FIN AF: 0.461

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.432

Gnomad OTH AF: 0.507

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

GnomAD4 genome AF: 0.476 AC: 72054 AN: 151324 Hom.: 17551 Cov.: 29 AF XY: 0.478 AC XY: 35317 AN XY: 73896

African (AFR) AF: 0.571 AC: 23538 AN: 41202

American (AMR) AF: 0.453 AC: 6885 AN: 15184

Ashkenazi Jewish (ASJ) AF: 0.538 AC: 1864 AN: 3462

East Asian (EAS) AF: 0.305 AC: 1560 AN: 5114

South Asian (SAS) AF: 0.537 AC: 2563 AN: 4774

European-Finnish (FIN) AF: 0.461 AC: 4825 AN: 10466

Middle Eastern (MID) AF: 0.479 AC: 140 AN: 292

European-Non Finnish (NFE) AF: 0.432 AC: 29268 AN: 67814

Other (OTH) AF: 0.507 AC: 1067 AN: 2106

Alfa AF: 0.453 Hom.: 5865

Bravo AF: 0.478

Asia WGS AF: 0.430 AC: 1491 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.36
DANN	Benign	0.47
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs558473; hg19: chr4-13984315;