rs2416682

Variant names:

• chr9-118689091-A-G
• rs2416682
• ENST00000450292.1:n.135-1088T>C

Variant summary

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

The ENST00000450292.1(ENSG00000225050):​n.135-1088T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.482 in 151,992 control chromosomes in the GnomAD database, including 17,823 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 0.48 (17823 hom., cov: 32)
• Consequence: ENSG00000225050 ENST00000450292.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.865
• Publications: 2 publications found

Genes affected

ENSG00000225050 (HGNC:):

LINC02578 (HGNC:53750): (long intergenic non-protein coding RNA 2578)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.491 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02578	NR_151725.1	n.173+5846A>G		intron_variant	Intron 2 of 3
LOC102724929	XR_007061892.1	n.796-1088T>C		intron_variant	Intron 5 of 5
LOC102724929	XR_428592.5	n.177-1088T>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000225050	ENST00000450292.1	n.135-1088T>C		intron_variant	Intron 1 of 1	2
ENSG00000225050	ENST00000670605.2	n.562-1088T>C		intron_variant	Intron 2 of 2
ENSG00000225050	ENST00000819557.1	n.379-1088T>C		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.482 AC: 73204 AN: 151874 Hom.: 17807 Cov.: 32

Gnomad AFR AF: 0.445

Gnomad AMI AF: 0.587

Gnomad AMR AF: 0.495

Gnomad ASJ AF: 0.561

Gnomad EAS AF: 0.472

Gnomad SAS AF: 0.507

Gnomad FIN AF: 0.473

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.496

Gnomad OTH AF: 0.507

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

GnomAD4 genome AF: 0.482 AC: 73261 AN: 151992 Hom.: 17823 Cov.: 32 AF XY: 0.483 AC XY: 35841 AN XY: 74268

African (AFR) AF: 0.445 AC: 18424 AN: 41442

American (AMR) AF: 0.495 AC: 7557 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.561 AC: 1946 AN: 3470

East Asian (EAS) AF: 0.472 AC: 2429 AN: 5146

South Asian (SAS) AF: 0.508 AC: 2448 AN: 4820

European-Finnish (FIN) AF: 0.473 AC: 4987 AN: 10554

Middle Eastern (MID) AF: 0.531 AC: 156 AN: 294

European-Non Finnish (NFE) AF: 0.496 AC: 33707 AN: 67970

Other (OTH) AF: 0.507 AC: 1072 AN: 2114

Alfa AF: 0.495 Hom.: 9869

Bravo AF: 0.483

Asia WGS AF: 0.517 AC: 1801 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.5
DANN	Benign	0.57
PhyloP100		0.86

Splicing

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

Other links and lift over

dbSNP: rs2416682; hg19: chr9-121451369;