2-8301605-C-G

Variant names:

• chr2-8301605-C-G
• rs13416555
• ENST00000430192.5:n.90-1812G>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 13 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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.279 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000430192.5. 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
	LINC00299	NR_034135.1		n.330-1812G>C		intron	N/A
	LINC00299	NR_152741.1		n.454-1812G>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00299	ENST00000430192.5	TSL:1	n.90-1812G>C		intron	N/A
	LINC00299	ENST00000442956.1	TSL:2	n.454-1812G>C		intron	N/A
	LINC00299	ENST00000668369.1		n.*204G>C		downstream_gene	N/A

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

African (AFR) AF: 0.115 AC: 4773 AN: 41398

American (AMR) AF: 0.258 AC: 3921 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.175 AC: 605 AN: 3466

East Asian (EAS) AF: 0.273 AC: 1395 AN: 5118

South Asian (SAS) AF: 0.254 AC: 1221 AN: 4804

European-Finnish (FIN) AF: 0.351 AC: 3660 AN: 10442

Middle Eastern (MID) AF: 0.171 AC: 50 AN: 292

European-Non Finnish (NFE) AF: 0.282 AC: 19133 AN: 67824

Other (OTH) AF: 0.227 AC: 475 AN: 2096

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.54
DANN	Benign	0.41
PhyloP100		-1.5

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs13416555;

hg19: chr2-8441735;