ENST00000428651.2:n.159+14514A>G

Variant names:

• chr2-156240264-T-C
• rs17188434
• ENST00000428651.2:n.159+14514A>G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000428651.2(LINC01876):​n.159+14514A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0443 in 152,312 control chromosomes in the GnomAD database, including 217 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 0.044 (217 hom., cov: 33)
• Consequence: LINC01876 ENST00000428651.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.869
• Publications: 25 publications found

Genes affected

LINC01876 (HGNC:52695): (long intergenic non-protein coding RNA 1876)

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.2).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0665 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01876	NR_110249.2	n.154+14514A>G		intron_variant	Intron 1 of 3
LINC01876	NR_110250.2	n.154+14514A>G		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01876	ENST00000428651.2	n.159+14514A>G		intron_variant	Intron 1 of 3	5
LINC01876	ENST00000635799.1	n.152+14514A>G		intron_variant	Intron 1 of 4	5
LINC01876	ENST00000636956.1	n.174-12260A>G		intron_variant	Intron 1 of 5	5

Frequencies

GnomAD3 genomes AF: 0.0443 AC: 6746 AN: 152194 Hom.: 217 Cov.: 33

Gnomad AFR AF: 0.0110

Gnomad AMI AF: 0.0395

Gnomad AMR AF: 0.0532

Gnomad ASJ AF: 0.0397

Gnomad EAS AF: 0.0104

Gnomad SAS AF: 0.0345

Gnomad FIN AF: 0.0306

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0681

Gnomad OTH AF: 0.0540

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

GnomAD4 genome AF: 0.0443 AC: 6743 AN: 152312 Hom.: 217 Cov.: 33 AF XY: 0.0420 AC XY: 3128 AN XY: 74470

African (AFR) AF: 0.0109 AC: 454 AN: 41574

American (AMR) AF: 0.0531 AC: 812 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0397 AC: 138 AN: 3472

East Asian (EAS) AF: 0.0104 AC: 54 AN: 5190

South Asian (SAS) AF: 0.0344 AC: 166 AN: 4830

European-Finnish (FIN) AF: 0.0306 AC: 325 AN: 10624

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0681 AC: 4632 AN: 68018

Other (OTH) AF: 0.0535 AC: 113 AN: 2114

Alfa AF: 0.0600 Hom.: 905

Bravo AF: 0.0441

Asia WGS AF: 0.0200 AC: 71 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.20
CADD	Benign	17
DANN	Benign	0.77
PhyloP100		0.87

Splicing

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

Other links and lift over

dbSNP: rs17188434; hg19: chr2-157096776;