rs111426949

Positions:

• chr5-10512585-C-T

Variant summary

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

The NR_134289.1(LINC02213):​n.330-6010G>A 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 0.063 in 152,222 control chromosomes in the GnomAD database, including 331 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 0.063 (331 hom., cov: 32)
• Consequence: LINC02213 NR_134289.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02

Genes affected

LINC02213 (HGNC:53080): (long intergenic non-protein coding RNA 2213)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0743 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02213	NR_134289.1	n.330-6010G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02213	ENST00000504650.2	n.330-6010G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.0630 AC: 9578 AN: 152104 Hom.: 330 Cov.: 32

Gnomad AFR AF: 0.0765

Gnomad AMI AF: 0.104

Gnomad AMR AF: 0.0762

Gnomad ASJ AF: 0.0566

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0319

Gnomad FIN AF: 0.0356

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.0629

Gnomad OTH AF: 0.0518

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

GnomAD4 genome AF: 0.0630 AC: 9583 AN: 152222 Hom.: 331 Cov.: 32 AF XY: 0.0615 AC XY: 4578 AN XY: 74436

Gnomad4 AFR AF: 0.0765

Gnomad4 AMR AF: 0.0762

Gnomad4 ASJ AF: 0.0566

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0319

Gnomad4 FIN AF: 0.0356

Gnomad4 NFE AF: 0.0629

Gnomad4 OTH AF: 0.0512

Alfa AF: 0.0673 Hom.: 57

Bravo AF: 0.0664

Asia WGS AF: 0.0230 AC: 79 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.65
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs111426949; hg19: chr5-10512697;