rs10174949

Variant names:

• chr2-8302118-G-A
• rs10174949
• ENST00000430192.5:n.90-2325C>T

Your query was ambiguous. Multiple possible variants found:

• chr2-8302118-G-A
• chr2-8302118-G-T

Variant summary

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

The ENST00000668369.1(LINC00299):​n.406C>T variant causes a non coding transcript exon 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 ENST00000668369.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0390
• Publications: 26 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=-0.76).
• 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: ENST00000668369.1. 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.330-2325C>T		intron	N/A
	LINC00299	NR_152741.1		n.454-2325C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00299	ENST00000430192.5	TSL:1	n.90-2325C>T		intron	N/A
	LINC00299	ENST00000668369.1		n.406C>T		non_coding_transcript_exon	Exon 2 of 2
	LINC00299	ENST00000715734.1		n.1315C>T		non_coding_transcript_exon	Exon 8 of 8

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

African (AFR) AF: 0.0963 AC: 3992 AN: 41468

American (AMR) AF: 0.257 AC: 3922 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.174 AC: 605 AN: 3468

East Asian (EAS) AF: 0.272 AC: 1398 AN: 5134

South Asian (SAS) AF: 0.253 AC: 1217 AN: 4804

European-Finnish (FIN) AF: 0.354 AC: 3726 AN: 10524

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.283 AC: 19199 AN: 67902

Other (OTH) AF: 0.227 AC: 478 AN: 2108

Alfa AF: 0.258 Hom.: 14922

Bravo AF: 0.219

Asia WGS AF: 0.277 AC: 961 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	2.8
DANN	Benign	0.78
PhyloP100		-0.039

Splicing

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

Other links and lift over

dbSNP: rs10174949; hg19: chr2-8442248;