rs17188434

Positions:

• chr2-156240264-T-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NR_110249.2(LINC01876):​n.154+14514A>G 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 0.0443 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 NR_110249.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.869

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LINC01876	NR_110249.2	n.154+14514A>G		intron_variant, non_coding_transcript_variant
LINC01876	NR_110250.2	n.154+14514A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01876	ENST00000635799.1	n.152+14514A>G		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.0109

Gnomad4 AMR AF: 0.0531

Gnomad4 ASJ AF: 0.0397

Gnomad4 EAS AF: 0.0104

Gnomad4 SAS AF: 0.0344

Gnomad4 FIN AF: 0.0306

Gnomad4 NFE AF: 0.0681

Gnomad4 OTH AF: 0.0535

Alfa AF: 0.0620 Hom.: 405

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17188434; hg19: chr2-157096776;