rs558473

Positions:

• chr4-13982691-A-G

Variant summary

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

The ENST00000669061.1(LINC01182):​n.714-18130A>G 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 0.476 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 ENST00000669061.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.629

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01182	ENST00000669061.1	n.714-18130A>G		intron_variant, non_coding_transcript_variant
LINC01182	ENST00000657663.1	n.136-18130A>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.571

Gnomad4 AMR AF: 0.453

Gnomad4 ASJ AF: 0.538

Gnomad4 EAS AF: 0.305

Gnomad4 SAS AF: 0.537

Gnomad4 FIN AF: 0.461

Gnomad4 NFE AF: 0.432

Gnomad4 OTH AF: 0.507

Alfa AF: 0.455 Hom.: 3732

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs558473; hg19: chr4-13984315;