rs10174949

chr2-8302118-G-Achr2-8302118-G-T

Variant summary

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

The NR_034135.1(LINC00299):n.330-2325C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.229 in 151,892 control chromosomes in the GnomAD database, including 4,592 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 (4592 hom., cov: 30)
• Consequence: LINC00299 NR_034135.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0390

Genes affected

LINC00299 (HGNC:27940): (long intergenic non-protein coding RNA 299)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• 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	UniProt
LINC00299	NR_034135.1	n.330-2325C>T		intron_variant, non_coding_transcript_variant
LINC00299	NR_152741.1	n.454-2325C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00299	ENST00000430192.5	n.90-2325C>T		intron_variant, non_coding_transcript_variant		1
LINC00299	ENST00000668369.1	n.406C>T		non_coding_transcript_exon_variant	2/2
LINC00299	ENST00000442956.1	n.454-2325C>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.230 AC: 34846 AN: 151774 Hom.: 4597 Cov.: 30

Gnomad AFR AF: 0.0966

Gnomad AMI AF: 0.285

Gnomad AMR AF: 0.256

Gnomad ASJ AF: 0.174

Gnomad EAS AF: 0.272

Gnomad SAS AF: 0.254

Gnomad FIN AF: 0.354

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.283

Gnomad OTH AF: 0.226

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

GnomAD4 genome AF: 0.229 AC: 34846 AN: 151892 Hom.: 4592 Cov.: 30 AF XY: 0.232 AC XY: 17255 AN XY: 74226

Gnomad4 AFR AF: 0.0963

Gnomad4 AMR AF: 0.257

Gnomad4 ASJ AF: 0.174

Gnomad4 EAS AF: 0.272

Gnomad4 SAS AF: 0.253

Gnomad4 FIN AF: 0.354

Gnomad4 NFE AF: 0.283

Gnomad4 OTH AF: 0.227

Alfa AF: 0.264 Hom.: 9547

Bravo AF: 0.219

Asia WGS AF: 0.277 AC: 961 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
Cadd	Benign	2.8
Dann	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10174949; hg19: chr2-8442248;