2-8301605-C-G

Position:

• chr2-8301605-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000430192.5(LINC00299):​n.90-1812G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.234 in 151,566 control chromosomes in the GnomAD database, including 4,625 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 0.23 (4625 hom., cov: 30)
• Consequence: LINC00299 ENST00000430192.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.54

Genes affected

LINC00299 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.279 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC00299	NR_034135.1	n.330-1812G>C		intron_variant
LINC00299	NR_152741.1	n.454-1812G>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC00299	ENST00000430192.5	n.90-1812G>C		intron_variant		1
LINC00299	ENST00000442956.1	n.454-1812G>C		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.234 AC: 35486 AN: 151448 Hom.: 4628 Cov.: 30

Gnomad AFR AF: 0.116

Gnomad AMI AF: 0.284

Gnomad AMR AF: 0.257

Gnomad ASJ AF: 0.175

Gnomad EAS AF: 0.272

Gnomad SAS AF: 0.254

Gnomad FIN AF: 0.351

Gnomad MID AF: 0.178

Gnomad NFE AF: 0.282

Gnomad OTH AF: 0.226

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

GnomAD4 genome AF: 0.234 AC: 35491 AN: 151566 Hom.: 4625 Cov.: 30 AF XY: 0.237 AC XY: 17521 AN XY: 74052

Gnomad4 AFR AF: 0.115

Gnomad4 AMR AF: 0.258

Gnomad4 ASJ AF: 0.175

Gnomad4 EAS AF: 0.273

Gnomad4 SAS AF: 0.254

Gnomad4 FIN AF: 0.351

Gnomad4 NFE AF: 0.282

Gnomad4 OTH AF: 0.227

Alfa AF: 0.148 Hom.: 284

Bravo AF: 0.226

Asia WGS AF: 0.277 AC: 964 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.54
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13416555; hg19: chr2-8441735;