rs10177924

Positions:

• chr2-156077041-A-G

Variant summary

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

The NR_110249.2(LINC01876):​n.155-52465T>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 0.279 in 152,034 control chromosomes in the GnomAD database, including 6,088 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 0.28 (6088 hom., cov: 32)
• Consequence: LINC01876 NR_110249.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.359

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=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.305 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01876	NR_110249.2	n.155-52465T>C		intron_variant, non_coding_transcript_variant
LINC01876	NR_110250.2	n.155-52434T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01876	ENST00000635799.1	n.153-52465T>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.279 AC: 42398 AN: 151916 Hom.: 6092 Cov.: 32

Gnomad AFR AF: 0.261

Gnomad AMI AF: 0.375

Gnomad AMR AF: 0.218

Gnomad ASJ AF: 0.293

Gnomad EAS AF: 0.127

Gnomad SAS AF: 0.319

Gnomad FIN AF: 0.333

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.302

Gnomad OTH AF: 0.273

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

GnomAD4 genome AF: 0.279 AC: 42400 AN: 152034 Hom.: 6088 Cov.: 32 AF XY: 0.279 AC XY: 20700 AN XY: 74312

Gnomad4 AFR AF: 0.261

Gnomad4 AMR AF: 0.218

Gnomad4 ASJ AF: 0.293

Gnomad4 EAS AF: 0.126

Gnomad4 SAS AF: 0.318

Gnomad4 FIN AF: 0.333

Gnomad4 NFE AF: 0.302

Gnomad4 OTH AF: 0.271

Alfa AF: 0.294 Hom.: 9470

Bravo AF: 0.267

Asia WGS AF: 0.257 AC: 891 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.1
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: rs10177924; hg19: chr2-156933553;