rs7587138

Variant names:

• chr2-46429950-G-A
• rs7587138
• ENST00000449601.6:n.172+671G>A

Variant summary

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

The ENST00000449601.6(LINC02583):​n.172+671G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.536 in 152,066 control chromosomes in the GnomAD database, including 22,064 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 0.54 (22064 hom., cov: 32)
• Consequence: LINC02583 ENST00000449601.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.258
• Publications: 5 publications found

Genes affected

LINC02583 (HGNC:53812): (long intergenic non-protein coding RNA 2583)

ENSG00000284608 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.574 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02583	NR_103805.1	n.90+671G>A		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02583	ENST00000449601.6	n.172+671G>A		intron_variant	Intron 1 of 3	1
LINC02583	ENST00000416466.3	n.191-226G>A		intron_variant	Intron 1 of 3	2
ENSG00000284608	ENST00000432241.5	n.86-226G>A		intron_variant	Intron 1 of 4	3

Frequencies

GnomAD3 genomes AF: 0.536 AC: 81455 AN: 151948 Hom.: 22035 Cov.: 32

Gnomad AFR AF: 0.580

Gnomad AMI AF: 0.328

Gnomad AMR AF: 0.546

Gnomad ASJ AF: 0.454

Gnomad EAS AF: 0.586

Gnomad SAS AF: 0.485

Gnomad FIN AF: 0.536

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.514

Gnomad OTH AF: 0.532

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

GnomAD4 genome AF: 0.536 AC: 81540 AN: 152066 Hom.: 22064 Cov.: 32 AF XY: 0.537 AC XY: 39932 AN XY: 74320

African (AFR) AF: 0.580 AC: 24064 AN: 41486

American (AMR) AF: 0.546 AC: 8353 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.454 AC: 1576 AN: 3470

East Asian (EAS) AF: 0.586 AC: 3034 AN: 5176

South Asian (SAS) AF: 0.485 AC: 2339 AN: 4824

European-Finnish (FIN) AF: 0.536 AC: 5661 AN: 10556

Middle Eastern (MID) AF: 0.493 AC: 144 AN: 292

European-Non Finnish (NFE) AF: 0.514 AC: 34946 AN: 67954

Other (OTH) AF: 0.534 AC: 1124 AN: 2106

Alfa AF: 0.522 Hom.: 89589

Bravo AF: 0.542

Asia WGS AF: 0.548 AC: 1905 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	6.5
DANN	Benign	0.92
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs7587138; hg19: chr2-46657089;