2-8527521-C-T

Variant names:

• chr2-8527521-C-T
• rs12624227
• ENST00000648900.3:n.618-20884G>A

Variant summary

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

The ENST00000648900.3(LINC00299):​n.618-20884G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.624 in 151,944 control chromosomes in the GnomAD database, including 31,443 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 0.62 (31443 hom., cov: 31)
• Consequence: LINC00299 ENST00000648900.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.628
• Publications: 4 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=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.769 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00299	ENST00000648900.3	n.618-20884G>A		intron_variant	Intron 4 of 4
LINC00299	ENST00000650238.2	n.1106+17627G>A		intron_variant	Intron 4 of 4
LINC00299	ENST00000657091.2	n.59+47845G>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.624 AC: 94776 AN: 151826 Hom.: 31443 Cov.: 31

Gnomad AFR AF: 0.376

Gnomad AMI AF: 0.662

Gnomad AMR AF: 0.712

Gnomad ASJ AF: 0.748

Gnomad EAS AF: 0.589

Gnomad SAS AF: 0.790

Gnomad FIN AF: 0.763

Gnomad MID AF: 0.684

Gnomad NFE AF: 0.717

Gnomad OTH AF: 0.643

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

GnomAD4 genome AF: 0.624 AC: 94789 AN: 151944 Hom.: 31443 Cov.: 31 AF XY: 0.629 AC XY: 46691 AN XY: 74256

African (AFR) AF: 0.376 AC: 15548 AN: 41386

American (AMR) AF: 0.713 AC: 10883 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.748 AC: 2596 AN: 3472

East Asian (EAS) AF: 0.589 AC: 3044 AN: 5172

South Asian (SAS) AF: 0.790 AC: 3794 AN: 4804

European-Finnish (FIN) AF: 0.763 AC: 8064 AN: 10570

Middle Eastern (MID) AF: 0.690 AC: 203 AN: 294

European-Non Finnish (NFE) AF: 0.717 AC: 48707 AN: 67964

Other (OTH) AF: 0.640 AC: 1346 AN: 2104

Alfa AF: 0.656 Hom.: 6320

Bravo AF: 0.609

Asia WGS AF: 0.664 AC: 2309 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	6.7
DANN	Benign	0.66
PhyloP100		0.63

Splicing

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

Other links and lift over

dbSNP: rs12624227; hg19: chr2-8667651;