ENST00000417751.5:n.257-113052A>G

Variant names:

• chr2-13954666-T-C
• rs549213
• ENST00000417751.5:n.257-113052A>G

Variant summary

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

The ENST00000417751.5(LINC00276):​n.257-113052A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.328 in 151,962 control chromosomes in the GnomAD database, including 9,430 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 0.33 (9430 hom., cov: 32)
• Consequence: LINC00276 ENST00000417751.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.556
• Publications: 6 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=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.458 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000417751.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00276	ENST00000417751.5	TSL:2	n.257-113052A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.328 AC: 49841 AN: 151844 Hom.: 9420 Cov.: 32

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.309

Gnomad AMR AF: 0.466

Gnomad ASJ AF: 0.243

Gnomad EAS AF: 0.434

Gnomad SAS AF: 0.245

Gnomad FIN AF: 0.488

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.382

Gnomad OTH AF: 0.317

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

GnomAD4 genome AF: 0.328 AC: 49850 AN: 151962 Hom.: 9430 Cov.: 32 AF XY: 0.334 AC XY: 24801 AN XY: 74238

African (AFR) AF: 0.153 AC: 6366 AN: 41500

American (AMR) AF: 0.467 AC: 7112 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.243 AC: 841 AN: 3468

East Asian (EAS) AF: 0.435 AC: 2242 AN: 5152

South Asian (SAS) AF: 0.245 AC: 1182 AN: 4826

European-Finnish (FIN) AF: 0.488 AC: 5140 AN: 10522

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.382 AC: 25947 AN: 67950

Other (OTH) AF: 0.313 AC: 660 AN: 2108

Alfa AF: 0.359 Hom.: 9021

Bravo AF: 0.323

Asia WGS AF: 0.330 AC: 1146 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.4
DANN	Benign	0.76
PhyloP100		0.56

Splicing

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

Other links and lift over

dbSNP: rs549213; hg19: chr2-14094791;