rs2029099

Variant names:

• chr2-14256792-A-C
• rs2029099
• ENST00000418420.1:n.252-20842T>G

Your query was ambiguous. Multiple possible variants found:

• chr2-14256792-A-C
• chr2-14256792-A-T

Variant summary

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

The ENST00000418420.1(LINC00276):​n.252-20842T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.219 in 152,166 control chromosomes in the GnomAD database, including 4,999 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 0.22 (4999 hom., cov: 33)
• Consequence: LINC00276 ENST00000418420.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.688
• Publications: 3 publications found

Genes affected

LINC00276 (HGNC:38663): (long intergenic non-protein coding RNA 276)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.432 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000418420.1. 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
	LINC00276	NR_103814.2		n.252-20842T>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00276	ENST00000418420.1	TSL:1	n.252-20842T>G		intron	N/A
	LINC00276	ENST00000417751.5	TSL:2	n.256+60177T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.219 AC: 33327 AN: 152048 Hom.: 4981 Cov.: 33

Gnomad AFR AF: 0.368

Gnomad AMI AF: 0.129

Gnomad AMR AF: 0.328

Gnomad ASJ AF: 0.144

Gnomad EAS AF: 0.448

Gnomad SAS AF: 0.210

Gnomad FIN AF: 0.199

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0976

Gnomad OTH AF: 0.182

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

GnomAD4 genome AF: 0.219 AC: 33390 AN: 152166 Hom.: 4999 Cov.: 33 AF XY: 0.226 AC XY: 16807 AN XY: 74402

African (AFR) AF: 0.368 AC: 15268 AN: 41488

American (AMR) AF: 0.328 AC: 5013 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.144 AC: 500 AN: 3468

East Asian (EAS) AF: 0.447 AC: 2305 AN: 5156

South Asian (SAS) AF: 0.210 AC: 1014 AN: 4824

European-Finnish (FIN) AF: 0.199 AC: 2114 AN: 10606

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.0976 AC: 6640 AN: 68016

Other (OTH) AF: 0.183 AC: 387 AN: 2116

Alfa AF: 0.127 Hom.: 1742

Bravo AF: 0.240

Asia WGS AF: 0.315 AC: 1094 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.9
DANN	Benign	0.81
PhyloP100		-0.69

Splicing

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

Other links and lift over

dbSNP: rs2029099; hg19: chr2-14396916;