rs1356743

Positions:

• chr2-156199390-C-T

Variant summary

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

The NR_110249.2(LINC01876):​n.154+55388G>A 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 0.465 in 151,852 control chromosomes in the GnomAD database, including 19,180 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 0.46 (19180 hom., cov: 32)
• Consequence: LINC01876 NR_110249.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.643

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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.76 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC01876	NR_110249.2	n.154+55388G>A		intron_variant, non_coding_transcript_variant
LINC01876	NR_110250.2	n.154+55388G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01876	ENST00000635799.1	n.152+55388G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.465 AC: 70496 AN: 151734 Hom.: 19120 Cov.: 32

Gnomad AFR AF: 0.767

Gnomad AMI AF: 0.241

Gnomad AMR AF: 0.343

Gnomad ASJ AF: 0.471

Gnomad EAS AF: 0.343

Gnomad SAS AF: 0.389

Gnomad FIN AF: 0.331

Gnomad MID AF: 0.334

Gnomad NFE AF: 0.347

Gnomad OTH AF: 0.430

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

GnomAD4 genome AF: 0.465 AC: 70611 AN: 151852 Hom.: 19180 Cov.: 32 AF XY: 0.462 AC XY: 34242 AN XY: 74182

Gnomad4 AFR AF: 0.767

Gnomad4 AMR AF: 0.343

Gnomad4 ASJ AF: 0.471

Gnomad4 EAS AF: 0.343

Gnomad4 SAS AF: 0.390

Gnomad4 FIN AF: 0.331

Gnomad4 NFE AF: 0.347

Gnomad4 OTH AF: 0.431

Alfa AF: 0.419 Hom.: 2363

Bravo AF: 0.479

Asia WGS AF: 0.402 AC: 1401 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	5.7
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1356743; hg19: chr2-157055902;