chr2-8485976-C-T

Variant names:

• chr2-8485976-C-T
• rs7581641
• ENST00000655671.1:n.48+2026G>A

Variant summary

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

The ENST00000655671.1(LINC00299):​n.48+2026G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.101 in 152,208 control chromosomes in the GnomAD database, including 1,692 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 0.10 (1692 hom., cov: 32)
• Consequence: LINC00299 ENST00000655671.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.61
• 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 (AFR) allele frequency at 95% confidence interval = 0.269 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000655671.1. 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
	LINC00299	ENST00000655671.1		n.48+2026G>A		intron	N/A
	LINC00299	ENST00000657091.2		n.59+89390G>A		intron	N/A
	LINC00299	ENST00000661371.1		n.89+2026G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.101 AC: 15363 AN: 152090 Hom.: 1683 Cov.: 32

Gnomad AFR AF: 0.273

Gnomad AMI AF: 0.0121

Gnomad AMR AF: 0.0586

Gnomad ASJ AF: 0.0458

Gnomad EAS AF: 0.0449

Gnomad SAS AF: 0.0928

Gnomad FIN AF: 0.0268

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0270

Gnomad OTH AF: 0.0934

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

GnomAD4 genome AF: 0.101 AC: 15412 AN: 152208 Hom.: 1692 Cov.: 32 AF XY: 0.101 AC XY: 7547 AN XY: 74428

African (AFR) AF: 0.273 AC: 11318 AN: 41478

American (AMR) AF: 0.0586 AC: 897 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.0458 AC: 159 AN: 3470

East Asian (EAS) AF: 0.0448 AC: 232 AN: 5182

South Asian (SAS) AF: 0.0923 AC: 445 AN: 4822

European-Finnish (FIN) AF: 0.0268 AC: 285 AN: 10616

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.0270 AC: 1835 AN: 68018

Other (OTH) AF: 0.0986 AC: 208 AN: 2110

Alfa AF: 0.0499 Hom.: 273

Bravo AF: 0.109

Asia WGS AF: 0.109 AC: 381 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	0.038
DANN	Benign	0.30
PhyloP100		-3.6

Splicing

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

Other links and lift over

dbSNP: rs7581641; hg19: chr2-8626106;