ENST00000504650.2:n.330-5643C>T

Variant names:

• chr5-10512218-G-A
• rs1971391
• ENST00000504650.2:n.330-5643C>T

Variant summary

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

The ENST00000504650.2(LINC02213):​n.330-5643C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.464 in 151,984 control chromosomes in the GnomAD database, including 16,500 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 0.46 (16500 hom., cov: 33)
• Consequence: LINC02213 ENST00000504650.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.535
• Publications: 4 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=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.547 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02213	NR_134289.1	n.330-5643C>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02213	ENST00000504650.2	n.330-5643C>T		intron_variant	Intron 1 of 2	3
ROPN1L	ENST00000718290.1	n.700-29767G>A		intron_variant	Intron 3 of 5

Frequencies

GnomAD3 genomes AF: 0.464 AC: 70497 AN: 151866 Hom.: 16484 Cov.: 33

Gnomad AFR AF: 0.497

Gnomad AMI AF: 0.382

Gnomad AMR AF: 0.457

Gnomad ASJ AF: 0.466

Gnomad EAS AF: 0.518

Gnomad SAS AF: 0.564

Gnomad FIN AF: 0.415

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.442

Gnomad OTH AF: 0.474

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

GnomAD4 genome AF: 0.464 AC: 70559 AN: 151984 Hom.: 16500 Cov.: 33 AF XY: 0.463 AC XY: 34385 AN XY: 74278

African (AFR) AF: 0.497 AC: 20611 AN: 41434

American (AMR) AF: 0.457 AC: 6979 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.466 AC: 1619 AN: 3472

East Asian (EAS) AF: 0.518 AC: 2683 AN: 5176

South Asian (SAS) AF: 0.564 AC: 2717 AN: 4814

European-Finnish (FIN) AF: 0.415 AC: 4366 AN: 10532

Middle Eastern (MID) AF: 0.534 AC: 157 AN: 294

European-Non Finnish (NFE) AF: 0.442 AC: 30073 AN: 67972

Other (OTH) AF: 0.477 AC: 1006 AN: 2108

Alfa AF: 0.449 Hom.: 59585

Bravo AF: 0.465

Asia WGS AF: 0.523 AC: 1819 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.3
DANN	Benign	0.28
PhyloP100		0.54

Splicing

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

Other links and lift over

dbSNP: rs1971391; hg19: chr5-10512330;