2-113337702-C-T

Position:

• chr2-113337702-C-T

Variant summary

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

The NR_183358.1(LINC02966):​n.615+8925C>T variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.246

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02966	NR_183358.1	n.615+8925C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02966	ENST00000690999.1	n.644+8925C>T		intron_variant, non_coding_transcript_variant
LINC02966	ENST00000653674.1	n.281+8925C>T		intron_variant, non_coding_transcript_variant
LINC02966	ENST00000691381.1	n.530+12149C>T		intron_variant, non_coding_transcript_variant
LINC02966	ENST00000700925.1	n.580+8925C>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.264

Gnomad4 AMR AF: 0.647

Gnomad4 ASJ AF: 0.548

Gnomad4 EAS AF: 0.695

Gnomad4 SAS AF: 0.502

Gnomad4 FIN AF: 0.618

Gnomad4 NFE AF: 0.588

Gnomad4 OTH AF: 0.540

Alfa AF: 0.575 Hom.: 41528

Bravo AF: 0.502

Asia WGS AF: 0.593 AC: 2061 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1191684; hg19: chr2-114095279;