rs13008689

Variant names:

• chr2-8390126-G-A
• rs13008689
• ENST00000655671.1:n.444+1827C>T

Your query was ambiguous. Multiple possible variants found:

• chr2-8390126-G-A
• chr2-8390126-G-T

Variant summary

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

The ENST00000655671.1(LINC00299):​n.444+1827C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.348 in 152,014 control chromosomes in the GnomAD database, including 9,728 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 0.35 (9728 hom., cov: 31)
• Consequence: LINC00299 ENST00000655671.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0140
• Publications: 14 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=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.396 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	ENST00000655671.1	n.444+1827C>T		intron_variant	Intron 3 of 6
LINC00299	ENST00000661371.1	n.485+1827C>T		intron_variant	Intron 3 of 5
LINC00299	ENST00000669954.1	n.571+1827C>T		intron_variant	Intron 3 of 7

Frequencies

GnomAD3 genomes AF: 0.348 AC: 52857 AN: 151896 Hom.: 9723 Cov.: 31

Gnomad AFR AF: 0.232

Gnomad AMI AF: 0.413

Gnomad AMR AF: 0.370

Gnomad ASJ AF: 0.336

Gnomad EAS AF: 0.381

Gnomad SAS AF: 0.410

Gnomad FIN AF: 0.479

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.387

Gnomad OTH AF: 0.332

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

GnomAD4 genome AF: 0.348 AC: 52896 AN: 152014 Hom.: 9728 Cov.: 31 AF XY: 0.355 AC XY: 26348 AN XY: 74310

African (AFR) AF: 0.232 AC: 9611 AN: 41412

American (AMR) AF: 0.371 AC: 5665 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.336 AC: 1163 AN: 3462

East Asian (EAS) AF: 0.380 AC: 1968 AN: 5174

South Asian (SAS) AF: 0.411 AC: 1982 AN: 4818

European-Finnish (FIN) AF: 0.479 AC: 5066 AN: 10586

Middle Eastern (MID) AF: 0.306 AC: 90 AN: 294

European-Non Finnish (NFE) AF: 0.387 AC: 26281 AN: 67972

Other (OTH) AF: 0.329 AC: 694 AN: 2112

Alfa AF: 0.369 Hom.: 31202

Bravo AF: 0.333

Asia WGS AF: 0.387 AC: 1348 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.2
DANN	Benign	0.66
PhyloP100		-0.014

Splicing

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

Other links and lift over

dbSNP: rs13008689; hg19: chr2-8530256;