2-8132890-G-C

Variant names:

• chr2-8132890-G-C
• rs181130
• ENST00000430192.5:n.714-72485C>G

Variant summary

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

The ENST00000430192.5(LINC00299):​n.714-72485C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.871 in 152,290 control chromosomes in the GnomAD database, including 58,517 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 0.87 (58517 hom., cov: 34)
• Consequence: LINC00299 ENST00000430192.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.142
• Publications: 5 publications found

Genes affected

LINC00299 (HGNC:27940): (long intergenic non-protein coding RNA 299)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.952 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000430192.5. 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
	LINC00299	NR_034135.1		n.954-72485C>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00299	ENST00000430192.5	TSL:1	n.714-72485C>G		intron	N/A
	LINC00299	ENST00000456681.1	TSL:3	n.346+144849C>G		intron	N/A
	LINC00299	ENST00000657310.1		n.356-72485C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.871 AC: 132565 AN: 152172 Hom.: 58477 Cov.: 34

Gnomad AFR AF: 0.959

Gnomad AMI AF: 0.873

Gnomad AMR AF: 0.686

Gnomad ASJ AF: 0.853

Gnomad EAS AF: 0.646

Gnomad SAS AF: 0.768

Gnomad FIN AF: 0.886

Gnomad MID AF: 0.873

Gnomad NFE AF: 0.882

Gnomad OTH AF: 0.864

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

GnomAD4 genome AF: 0.871 AC: 132652 AN: 152290 Hom.: 58517 Cov.: 34 AF XY: 0.865 AC XY: 64411 AN XY: 74460

African (AFR) AF: 0.960 AC: 39905 AN: 41586

American (AMR) AF: 0.685 AC: 10479 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.853 AC: 2960 AN: 3472

East Asian (EAS) AF: 0.645 AC: 3331 AN: 5164

South Asian (SAS) AF: 0.767 AC: 3705 AN: 4828

European-Finnish (FIN) AF: 0.886 AC: 9394 AN: 10606

Middle Eastern (MID) AF: 0.878 AC: 258 AN: 294

European-Non Finnish (NFE) AF: 0.882 AC: 60005 AN: 68028

Other (OTH) AF: 0.862 AC: 1819 AN: 2110

Alfa AF: 0.875 Hom.: 6831

Bravo AF: 0.858

Asia WGS AF: 0.697 AC: 2423 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	4.3
DANN	Benign	0.68
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs181130; hg19: chr2-8273020;