2-113337702-C-T

Variant names:

• chr2-113337702-C-T
• rs1191684
• ENST00000653674.1:n.281+8925C>T

Variant summary

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

The NR_183358.1(LINC02966):​n.615+8925C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.508 in 152,034 control chromosomes in the GnomAD database, including 21,481 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 0.51 (21481 hom., cov: 32)
• Consequence: LINC02966 NR_183358.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.246
• Publications: 6 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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.676 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_183358.1. 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
	LINC02966	NR_183358.1		n.615+8925C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02966	ENST00000653674.1		n.281+8925C>T		intron	N/A
	LINC02966	ENST00000690999.2		n.644+8925C>T		intron	N/A
	LINC02966	ENST00000691381.2		n.530+12149C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.508 AC: 77153 AN: 151916 Hom.: 21474 Cov.: 32

Gnomad AFR AF: 0.264

Gnomad AMI AF: 0.770

Gnomad AMR AF: 0.647

Gnomad ASJ AF: 0.548

Gnomad EAS AF: 0.694

Gnomad SAS AF: 0.502

Gnomad FIN AF: 0.618

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.588

Gnomad OTH AF: 0.538

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

GnomAD4 genome AF: 0.508 AC: 77186 AN: 152034 Hom.: 21481 Cov.: 32 AF XY: 0.512 AC XY: 38047 AN XY: 74330

African (AFR) AF: 0.264 AC: 10924 AN: 41434

American (AMR) AF: 0.647 AC: 9895 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.548 AC: 1900 AN: 3466

East Asian (EAS) AF: 0.695 AC: 3593 AN: 5172

South Asian (SAS) AF: 0.502 AC: 2418 AN: 4812

European-Finnish (FIN) AF: 0.618 AC: 6532 AN: 10578

Middle Eastern (MID) AF: 0.507 AC: 149 AN: 294

European-Non Finnish (NFE) AF: 0.588 AC: 39934 AN: 67968

Other (OTH) AF: 0.540 AC: 1139 AN: 2110

Alfa AF: 0.565 Hom.: 91417

Bravo AF: 0.502

Asia WGS AF: 0.593 AC: 2061 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	7.2
DANN	Benign	0.48
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs1191684; hg19: chr2-114095279;