2-113332835-A-G

Variant names:

• chr2-113332835-A-G
• rs1823125
• ENST00000653674.1:n.281+4058A>G

Variant summary

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

The ENST00000653674.1(LINC02966):​n.281+4058A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.189 in 152,132 control chromosomes in the GnomAD database, including 2,955 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 0.19 (2955 hom., cov: 33)
• Consequence: LINC02966 ENST00000653674.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.595
• Publications: 16 publications found

Genes affected

LINC02966 (HGNC:56006): (long intergenic non-protein coding RNA 2966)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.244 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02966	NR_183358.1	n.615+4058A>G		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02966	ENST00000653674.1	n.281+4058A>G		intron_variant	Intron 2 of 3
LINC02966	ENST00000690999.2	n.644+4058A>G		intron_variant	Intron 2 of 3
LINC02966	ENST00000691381.2	n.530+7282A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.189 AC: 28704 AN: 152014 Hom.: 2956 Cov.: 33

Gnomad AFR AF: 0.115

Gnomad AMI AF: 0.138

Gnomad AMR AF: 0.158

Gnomad ASJ AF: 0.289

Gnomad EAS AF: 0.204

Gnomad SAS AF: 0.256

Gnomad FIN AF: 0.204

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.228

Gnomad OTH AF: 0.187

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

GnomAD4 genome AF: 0.189 AC: 28709 AN: 152132 Hom.: 2955 Cov.: 33 AF XY: 0.188 AC XY: 14016 AN XY: 74376

African (AFR) AF: 0.115 AC: 4764 AN: 41498

American (AMR) AF: 0.158 AC: 2423 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.289 AC: 1002 AN: 3472

East Asian (EAS) AF: 0.203 AC: 1050 AN: 5162

South Asian (SAS) AF: 0.256 AC: 1230 AN: 4812

European-Finnish (FIN) AF: 0.204 AC: 2162 AN: 10576

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.228 AC: 15477 AN: 67998

Other (OTH) AF: 0.187 AC: 395 AN: 2112

Alfa AF: 0.207 Hom.: 5345

Bravo AF: 0.181

Asia WGS AF: 0.201 AC: 698 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.90
DANN	Benign	0.49
PhyloP100		-0.59

Splicing

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

Other links and lift over

dbSNP: rs1823125; hg19: chr2-114090412;