rs7587138

chr2-46429950-G-A

Variant summary

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

The NR_103805.1(LINC02583):n.90+671G>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 0.536 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 NR_103805.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.258

Genes affected

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

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LINC02583	NR_103805.1	n.90+671G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02583	ENST00000449601.5	n.90+671G>A		intron_variant, non_coding_transcript_variant		1
	ENST00000517716.2	n.52-226G>A		intron_variant, non_coding_transcript_variant		5
LINC02583	ENST00000642724.1	n.57-226G>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.580

Gnomad4 AMR AF: 0.546

Gnomad4 ASJ AF: 0.454

Gnomad4 EAS AF: 0.586

Gnomad4 SAS AF: 0.485

Gnomad4 FIN AF: 0.536

Gnomad4 NFE AF: 0.514

Gnomad4 OTH AF: 0.534

Alfa AF: 0.517 Hom.: 41887

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7587138; hg19: chr2-46657089;