rs16889099

chr4-13730462-T-C

Variant summary

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

The NR_121681.1(LINC01182):n.281+72608T>C 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 0.089 in 152,220 control chromosomes in the GnomAD database, including 615 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 0.089 (615 hom., cov: 32)
• Consequence: LINC01182 NR_121681.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.915

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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.116 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01182	NR_121681.1	n.281+72608T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01182	ENST00000669061.1	n.548+72608T>C		intron_variant, non_coding_transcript_variant
LINC01182	ENST00000510907.5	n.281+72608T>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.0890 AC: 13535 AN: 152102 Hom.: 613 Cov.: 32

Gnomad AFR AF: 0.0861

Gnomad AMI AF: 0.146

Gnomad AMR AF: 0.0915

Gnomad ASJ AF: 0.0957

Gnomad EAS AF: 0.124

Gnomad SAS AF: 0.0976

Gnomad FIN AF: 0.124

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.0798

Gnomad OTH AF: 0.101

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

GnomAD4 genome AF: 0.0890 AC: 13553 AN: 152220 Hom.: 615 Cov.: 32 AF XY: 0.0920 AC XY: 6846 AN XY: 74428

Gnomad4 AFR AF: 0.0861

Gnomad4 AMR AF: 0.0918

Gnomad4 ASJ AF: 0.0957

Gnomad4 EAS AF: 0.124

Gnomad4 SAS AF: 0.0979

Gnomad4 FIN AF: 0.124

Gnomad4 NFE AF: 0.0799

Gnomad4 OTH AF: 0.101

Alfa AF: 0.0851 Hom.: 550

Bravo AF: 0.0865

Asia WGS AF: 0.105 AC: 364 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	8.2
Dann	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16889099; hg19: chr4-13732086;