rs2077411

Variant names:

• chr2-14225321-C-G
• rs2077411
• ENST00000417751.5:n.256+91648G>C

Variant summary

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

The ENST00000417751.5(LINC00276):​n.256+91648G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.405 in 151,818 control chromosomes in the GnomAD database, including 12,918 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 0.40 (12918 hom., cov: 31)
• Consequence: LINC00276 ENST00000417751.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.163

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=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.442 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+91648G>C		intron_variant	Intron 2 of 4	2

Frequencies

GnomAD3 genomes AF: 0.405 AC: 61441 AN: 151700 Hom.: 12913 Cov.: 31

Gnomad AFR AF: 0.411

Gnomad AMI AF: 0.530

Gnomad AMR AF: 0.323

Gnomad ASJ AF: 0.390

Gnomad EAS AF: 0.170

Gnomad SAS AF: 0.253

Gnomad FIN AF: 0.406

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.446

Gnomad OTH AF: 0.433

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

GnomAD4 genome AF: 0.405 AC: 61473 AN: 151818 Hom.: 12918 Cov.: 31 AF XY: 0.396 AC XY: 29419 AN XY: 74198

Gnomad4 AFR AF: 0.411

Gnomad4 AMR AF: 0.323

Gnomad4 ASJ AF: 0.390

Gnomad4 EAS AF: 0.171

Gnomad4 SAS AF: 0.254

Gnomad4 FIN AF: 0.406

Gnomad4 NFE AF: 0.446

Gnomad4 OTH AF: 0.430

Alfa AF: 0.416 Hom.: 1660

Bravo AF: 0.396

Asia WGS AF: 0.245 AC: 854 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.5
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2077411; hg19: chr2-14365445;