2-14167405-A-G

Variant names:

• chr2-14167405-A-G
• rs1839206
• ENST00000417751.5:n.256+149564T>C

Variant summary

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

The ENST00000417751.5(LINC00276):​n.256+149564T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.675 in 151,458 control chromosomes in the GnomAD database, including 34,963 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 0.68 (34963 hom., cov: 32)
• Consequence: LINC00276 ENST00000417751.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.315
• 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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.733 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00276	ENST00000417751.5	n.256+149564T>C		intron_variant	Intron 2 of 4	2

Frequencies

GnomAD3 genomes AF: 0.675 AC: 102228 AN: 151340 Hom.: 34936 Cov.: 32

Gnomad AFR AF: 0.589

Gnomad AMI AF: 0.755

Gnomad AMR AF: 0.621

Gnomad ASJ AF: 0.669

Gnomad EAS AF: 0.626

Gnomad SAS AF: 0.651

Gnomad FIN AF: 0.727

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.738

Gnomad OTH AF: 0.637

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

GnomAD4 genome AF: 0.675 AC: 102308 AN: 151458 Hom.: 34963 Cov.: 32 AF XY: 0.673 AC XY: 49792 AN XY: 73990

African (AFR) AF: 0.589 AC: 24368 AN: 41350

American (AMR) AF: 0.621 AC: 9399 AN: 15144

Ashkenazi Jewish (ASJ) AF: 0.669 AC: 2313 AN: 3458

East Asian (EAS) AF: 0.625 AC: 3204 AN: 5126

South Asian (SAS) AF: 0.653 AC: 3147 AN: 4820

European-Finnish (FIN) AF: 0.727 AC: 7692 AN: 10574

Middle Eastern (MID) AF: 0.629 AC: 185 AN: 294

European-Non Finnish (NFE) AF: 0.738 AC: 49977 AN: 67686

Other (OTH) AF: 0.637 AC: 1336 AN: 2096

Alfa AF: 0.714 Hom.: 73650

Bravo AF: 0.665

Asia WGS AF: 0.659 AC: 2282 AN: 3456

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	8.2
DANN	Benign	0.85
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs1839206; hg19: chr2-14307530;