rs111426949

Variant names:

• chr5-10512585-C-T
• rs111426949
• ENST00000504650.2:n.330-6010G>A

Variant summary

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

The ENST00000504650.2(LINC02213):​n.330-6010G>A variant causes a intron 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 ENST00000504650.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02
• Publications: 3 publications found

Genes affected

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

ROPN1L (HGNC:24060): (rhophilin associated tail protein 1 like) This gene encodes a member of the ropporin family. The encoded protein is present in sperm and interacts with A-kinase anchoring protein, AKAP3, through the amphipathic helix region of AKAP3. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Oct 2014]

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LINC02213	NR_134289.1	n.330-6010G>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02213	ENST00000504650.2	n.330-6010G>A		intron_variant	Intron 1 of 2	3
ROPN1L	ENST00000718290.1	n.700-29400C>T		intron_variant	Intron 3 of 5

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

African (AFR) AF: 0.0765 AC: 3179 AN: 41540

American (AMR) AF: 0.0762 AC: 1165 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0566 AC: 196 AN: 3464

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5184

South Asian (SAS) AF: 0.0319 AC: 154 AN: 4828

European-Finnish (FIN) AF: 0.0356 AC: 378 AN: 10604

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.0629 AC: 4274 AN: 67996

Other (OTH) AF: 0.0512 AC: 108 AN: 2108

Alfa AF: 0.0674 Hom.: 206

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
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs111426949; hg19: chr5-10512697;