rs11616562

Variant names:

• chr13-84183890-A-G
• rs11616562
• ENST00000653443.1:n.197-54650A>G

Variant summary

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

The NR_046871.1(LINC00333):​n.42+43247A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0732 in 151,992 control chromosomes in the GnomAD database, including 504 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 0.073 (504 hom., cov: 32)
• Consequence: LINC00333 NR_046871.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.225

Genes affected

ENSG00000288016 (HGNC:):

LINC00333 (HGNC:42050): (long intergenic non-protein coding RNA 333)

ACMG classification

Verdict is Benign. Variant got -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 = 0.171 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00333	NR_046871.1	n.42+43247A>G		intron_variant	Intron 1 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000288016	ENST00000653443.1	n.197-54650A>G		intron_variant	Intron 1 of 4
ENSG00000288016	ENST00000654433.1	n.74+43243A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0731 AC: 11102 AN: 151874 Hom.: 502 Cov.: 32

Gnomad AFR AF: 0.0693

Gnomad AMI AF: 0.0395

Gnomad AMR AF: 0.139

Gnomad ASJ AF: 0.0514

Gnomad EAS AF: 0.180

Gnomad SAS AF: 0.0652

Gnomad FIN AF: 0.0629

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0559

Gnomad OTH AF: 0.0909

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

GnomAD4 genome AF: 0.0732 AC: 11133 AN: 151992 Hom.: 504 Cov.: 32 AF XY: 0.0754 AC XY: 5604 AN XY: 74300

Gnomad4 AFR AF: 0.0694

Gnomad4 AMR AF: 0.139

Gnomad4 ASJ AF: 0.0514

Gnomad4 EAS AF: 0.181

Gnomad4 SAS AF: 0.0659

Gnomad4 FIN AF: 0.0629

Gnomad4 NFE AF: 0.0559

Gnomad4 OTH AF: 0.0914

Alfa AF: 0.0592 Hom.: 227

Bravo AF: 0.0800

Asia WGS AF: 0.110 AC: 381 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	2.3
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11616562; hg19: chr13-84758025;