2-43131922-C-A

Variant names:

• chr2-43131922-C-A
• rs12466022
• ENST00000658582.2:n.1335C>A

Variant summary

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

The ENST00000658582.2(ENSG00000286796):​n.1335C>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: ENSG00000286796 ENST00000658582.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.801
• Publications: 50 publications found

Genes affected

ENSG00000286796 (HGNC:):

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000658582.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000286796	ENST00000658582.2		n.1335C>A		non_coding_transcript_exon	Exon 3 of 3
	ENSG00000286796	ENST00000669652.2		n.2399C>A		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000286796	ENST00000829606.1		n.1178C>A		non_coding_transcript_exon	Exon 4 of 4

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

African (AFR) AF: 0.368 AC: 15267 AN: 41452

American (AMR) AF: 0.275 AC: 4202 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.301 AC: 1044 AN: 3472

East Asian (EAS) AF: 0.260 AC: 1345 AN: 5178

South Asian (SAS) AF: 0.145 AC: 700 AN: 4828

European-Finnish (FIN) AF: 0.249 AC: 2641 AN: 10590

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.270 AC: 18355 AN: 67994

Other (OTH) AF: 0.286 AC: 603 AN: 2112

Alfa AF: 0.276 Hom.: 26268

Bravo AF: 0.302

Asia WGS AF: 0.205 AC: 713 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.24
DANN	Benign	0.79
PhyloP100		-0.80

Splicing

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

Other links and lift over

dbSNP: rs12466022; hg19: chr2-43359061;