rs6716573

Variant names:

• chr2-113283164-C-T
• rs6716573
• ENST00000803921.1:n.104+525C>T

Variant summary

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

The ENST00000803921.1(LINC02966):​n.104+525C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.265 in 152,182 control chromosomes in the GnomAD database, including 5,449 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 0.27 (5449 hom., cov: 33)
• Consequence: LINC02966 ENST00000803921.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.874
• Publications: 5 publications found

Genes affected

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

ENSG00000304529 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.271 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000803921.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02966	ENST00000803921.1		n.104+525C>T		intron	N/A
	LINC02966	ENST00000803934.1		n.460-508C>T		intron	N/A
	LINC02966	ENST00000803935.1		n.388+525C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.265 AC: 40285 AN: 152064 Hom.: 5435 Cov.: 33

Gnomad AFR AF: 0.274

Gnomad AMI AF: 0.219

Gnomad AMR AF: 0.271

Gnomad ASJ AF: 0.222

Gnomad EAS AF: 0.0789

Gnomad SAS AF: 0.247

Gnomad FIN AF: 0.276

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.274

Gnomad OTH AF: 0.286

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

GnomAD4 genome AF: 0.265 AC: 40334 AN: 152182 Hom.: 5449 Cov.: 33 AF XY: 0.264 AC XY: 19665 AN XY: 74406

African (AFR) AF: 0.275 AC: 11402 AN: 41522

American (AMR) AF: 0.270 AC: 4134 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.222 AC: 770 AN: 3472

East Asian (EAS) AF: 0.0787 AC: 408 AN: 5184

South Asian (SAS) AF: 0.247 AC: 1191 AN: 4826

European-Finnish (FIN) AF: 0.276 AC: 2918 AN: 10576

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.274 AC: 18632 AN: 67990

Other (OTH) AF: 0.288 AC: 610 AN: 2116

Alfa AF: 0.271 Hom.: 1307

Bravo AF: 0.266

Asia WGS AF: 0.206 AC: 720 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.3
DANN	Benign	0.78
PhyloP100		-0.87

Splicing

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

Other links and lift over

dbSNP: rs6716573; hg19: chr2-114040741;