rs1823125

Positions:

• chr2-113332835-A-G

Variant summary

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

The NR_183358.1(LINC02966):​n.615+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 NR_183358.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.595

Genes affected

LINC02966 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
LINC02966	NR_183358.1	n.615+4058A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02966	ENST00000653674.1	n.281+4058A>G		intron_variant
LINC02966	ENST00000690999.1	n.644+4058A>G		intron_variant
LINC02966	ENST00000691381.1	n.530+7282A>G		intron_variant
LINC02966	ENST00000700925.1	n.580+4058A>G		intron_variant

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

Gnomad4 AFR AF: 0.115

Gnomad4 AMR AF: 0.158

Gnomad4 ASJ AF: 0.289

Gnomad4 EAS AF: 0.203

Gnomad4 SAS AF: 0.256

Gnomad4 FIN AF: 0.204

Gnomad4 NFE AF: 0.228

Gnomad4 OTH AF: 0.187

Alfa AF: 0.204 Hom.: 918

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1823125; hg19: chr2-114090412;