chr2-156031988-C-G

Position:

• chr2-156031988-C-G

Variant summary

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

The NR_110249.2(LINC01876):​n.155-7412G>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 0.825 in 152,114 control chromosomes in the GnomAD database, including 52,909 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 0.83 (52909 hom., cov: 32)
• Consequence: LINC01876 NR_110249.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.40

Genes affected

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

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 = 0.905 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC01876	NR_110249.2	n.155-7412G>C		intron_variant, non_coding_transcript_variant
LINC01876	NR_110250.2	n.155-7381G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01876	ENST00000635799.1	n.153-7412G>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.825 AC: 125470 AN: 151996 Hom.: 52888 Cov.: 32

Gnomad AFR AF: 0.637

Gnomad AMI AF: 0.932

Gnomad AMR AF: 0.871

Gnomad ASJ AF: 0.880

Gnomad EAS AF: 0.804

Gnomad SAS AF: 0.853

Gnomad FIN AF: 0.917

Gnomad MID AF: 0.851

Gnomad NFE AF: 0.911

Gnomad OTH AF: 0.837

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

GnomAD4 genome AF: 0.825 AC: 125541 AN: 152114 Hom.: 52909 Cov.: 32 AF XY: 0.828 AC XY: 61577 AN XY: 74382

Gnomad4 AFR AF: 0.637

Gnomad4 AMR AF: 0.872

Gnomad4 ASJ AF: 0.880

Gnomad4 EAS AF: 0.804

Gnomad4 SAS AF: 0.854

Gnomad4 FIN AF: 0.917

Gnomad4 NFE AF: 0.911

Gnomad4 OTH AF: 0.834

Alfa AF: 0.889 Hom.: 33517

Bravo AF: 0.813

Asia WGS AF: 0.818 AC: 2843 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	0.20
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1918172; hg19: chr2-156888500;