rs12466022

chr2-43131922-C-Achr2-43131922-C-T

Variant summary

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

The ENST00000669652.1(ENSG00000286796):n.2383C>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.292 in 152,108 control chromosomes in the GnomAD database, including 6,683 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 0.29 (6683 hom., cov: 33)
• Consequence: ENST00000669652.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.801

Genes affected

(HGNC:):

LINC02580 (HGNC:53751): (long intergenic non-protein coding RNA 2580)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.363 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105374570	XR_940018.3	n.1296C>A		non_coding_transcript_exon_variant	3/3
LOC105374570	XR_007086297.1	n.1215C>A		non_coding_transcript_exon_variant	4/4
LOC105374570	XR_940019.3	n.1302C>A		non_coding_transcript_exon_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000669652.1	n.2383C>A		non_coding_transcript_exon_variant	2/2
LINC02580	ENST00000705257.1	n.185-33882G>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.292 AC: 44335 AN: 151990 Hom.: 6666 Cov.: 33

Gnomad AFR AF: 0.368

Gnomad AMI AF: 0.180

Gnomad AMR AF: 0.275

Gnomad ASJ AF: 0.301

Gnomad EAS AF: 0.259

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.249

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.270

Gnomad OTH AF: 0.287

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

GnomAD4 genome AF: 0.292 AC: 44403 AN: 152108 Hom.: 6683 Cov.: 33 AF XY: 0.288 AC XY: 21393 AN XY: 74346

Gnomad4 AFR AF: 0.368

Gnomad4 AMR AF: 0.275

Gnomad4 ASJ AF: 0.301

Gnomad4 EAS AF: 0.260

Gnomad4 SAS AF: 0.145

Gnomad4 FIN AF: 0.249

Gnomad4 NFE AF: 0.270

Gnomad4 OTH AF: 0.286

Alfa AF: 0.268 Hom.: 12223

Bravo AF: 0.302

Asia WGS AF: 0.205 AC: 713 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	0.24
Dann	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12466022; hg19: chr2-43359061;