chr12-126000924-A-G

Variant names:

• chr12-126000924-A-G
• rs225537
• ENST00000642407.1:n.511+13695A>G

Variant summary

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

The ENST00000642407.1(LINC02826):​n.511+13695A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.362 in 151,946 control chromosomes in the GnomAD database, including 11,445 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 0.36 (11445 hom., cov: 32)
• Consequence: LINC02826 ENST00000642407.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.775
• Publications: 0 publications found

Genes affected

LINC02826 (HGNC:54357): (long intergenic non-protein coding RNA 2826)

ENSG00000306956 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.58 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000642407.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02826	NR_183612.1		n.696+13695A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02826	ENST00000642407.1		n.511+13695A>G		intron	N/A
	LINC02826	ENST00000660252.1		n.2768-29A>G		intron	N/A
	LINC02826	ENST00000821911.1		n.326-11951A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.362 AC: 54971 AN: 151828 Hom.: 11421 Cov.: 32

Gnomad AFR AF: 0.586

Gnomad AMI AF: 0.208

Gnomad AMR AF: 0.281

Gnomad ASJ AF: 0.340

Gnomad EAS AF: 0.165

Gnomad SAS AF: 0.252

Gnomad FIN AF: 0.312

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.279

Gnomad OTH AF: 0.345

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

GnomAD4 genome AF: 0.362 AC: 55035 AN: 151946 Hom.: 11445 Cov.: 32 AF XY: 0.360 AC XY: 26739 AN XY: 74240

African (AFR) AF: 0.586 AC: 24283 AN: 41430

American (AMR) AF: 0.281 AC: 4292 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.340 AC: 1177 AN: 3464

East Asian (EAS) AF: 0.166 AC: 853 AN: 5152

South Asian (SAS) AF: 0.251 AC: 1209 AN: 4820

European-Finnish (FIN) AF: 0.312 AC: 3283 AN: 10532

Middle Eastern (MID) AF: 0.306 AC: 90 AN: 294

European-Non Finnish (NFE) AF: 0.279 AC: 18935 AN: 67960

Other (OTH) AF: 0.343 AC: 724 AN: 2110

Alfa AF: 0.338 Hom.: 1267

Bravo AF: 0.369

Asia WGS AF: 0.245 AC: 853 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.9
DANN	Benign	0.52
PhyloP100		-0.78

Splicing

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

Other links and lift over

dbSNP: rs225537; hg19: chr12-126485470;