chr2-14225321-C-G

Variant names:

• chr2-14225321-C-G
• rs2077411
• ENST00000417751.5:n.256+91648G>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+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
• Publications: 2 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=-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

African (AFR) AF: 0.411 AC: 17015 AN: 41410

American (AMR) AF: 0.323 AC: 4909 AN: 15212

Ashkenazi Jewish (ASJ) AF: 0.390 AC: 1351 AN: 3468

East Asian (EAS) AF: 0.171 AC: 880 AN: 5152

South Asian (SAS) AF: 0.254 AC: 1220 AN: 4806

European-Finnish (FIN) AF: 0.406 AC: 4282 AN: 10540

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.446 AC: 30296 AN: 67922

Other (OTH) AF: 0.430 AC: 904 AN: 2104

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
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs2077411; hg19: chr2-14365445;