2-8076274-C-T

Variant names:

• chr2-8076274-C-T
• rs1025053
• ENST00000430192.5:n.714-15869G>A

Variant summary

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

The ENST00000430192.5(LINC00299):​n.714-15869G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.57 in 152,114 control chromosomes in the GnomAD database, including 25,364 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 0.57 (25364 hom., cov: 33)
• Consequence: LINC00299 ENST00000430192.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.44
• 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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.714 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00299	NR_034135.1	n.954-15869G>A		intron_variant	Intron 7 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00299	ENST00000430192.5	n.714-15869G>A		intron_variant	Intron 6 of 7	1
LINC00299	ENST00000454043.2	n.153-15869G>A		intron_variant	Intron 1 of 2	4
LINC00299	ENST00000456681.1	n.347-96948G>A		intron_variant	Intron 1 of 3	3

Frequencies

GnomAD3 genomes AF: 0.569 AC: 86544 AN: 151994 Hom.: 25319 Cov.: 33

Gnomad AFR AF: 0.720

Gnomad AMI AF: 0.537

Gnomad AMR AF: 0.526

Gnomad ASJ AF: 0.500

Gnomad EAS AF: 0.569

Gnomad SAS AF: 0.483

Gnomad FIN AF: 0.466

Gnomad MID AF: 0.655

Gnomad NFE AF: 0.513

Gnomad OTH AF: 0.565

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

GnomAD4 genome AF: 0.570 AC: 86645 AN: 152114 Hom.: 25364 Cov.: 33 AF XY: 0.565 AC XY: 42040 AN XY: 74354

African (AFR) AF: 0.721 AC: 29938 AN: 41524

American (AMR) AF: 0.527 AC: 8052 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.500 AC: 1735 AN: 3468

East Asian (EAS) AF: 0.568 AC: 2939 AN: 5172

South Asian (SAS) AF: 0.482 AC: 2323 AN: 4822

European-Finnish (FIN) AF: 0.466 AC: 4922 AN: 10562

Middle Eastern (MID) AF: 0.663 AC: 195 AN: 294

European-Non Finnish (NFE) AF: 0.513 AC: 34862 AN: 67960

Other (OTH) AF: 0.563 AC: 1190 AN: 2112

Alfa AF: 0.538 Hom.: 29584

Bravo AF: 0.582

Asia WGS AF: 0.523 AC: 1816 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.085
DANN	Benign	0.21
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs1025053; hg19: chr2-8216404;