chr2-14167405-A-G

Position:

• chr2-14167405-A-G

Variant summary

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

The ENST00000417751.5(LINC00276):​n.256+149564T>C 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 0.675 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.315

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00276	ENST00000417751.5	n.256+149564T>C		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.589

Gnomad4 AMR AF: 0.621

Gnomad4 ASJ AF: 0.669

Gnomad4 EAS AF: 0.625

Gnomad4 SAS AF: 0.653

Gnomad4 FIN AF: 0.727

Gnomad4 NFE AF: 0.738

Gnomad4 OTH AF: 0.637

Alfa AF: 0.725 Hom.: 38883

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1839206; hg19: chr2-14307530;