chr2-156066908-T-C

Position:

• chr2-156066908-T-C

Variant summary

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

The NR_110249.2(LINC01876):​n.155-42332A>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 0.0624 in 152,198 control chromosomes in the GnomAD database, including 405 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 0.062 (405 hom., cov: 32)
• Consequence: LINC01876 NR_110249.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.13

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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.11 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01876	NR_110249.2	n.155-42332A>G		intron_variant, non_coding_transcript_variant
LINC01876	NR_110250.2	n.155-42301A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01876	ENST00000635799.1	n.153-42332A>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.0624 AC: 9483 AN: 152080 Hom.: 405 Cov.: 32

Gnomad AFR AF: 0.112

Gnomad AMI AF: 0.0493

Gnomad AMR AF: 0.0429

Gnomad ASJ AF: 0.0714

Gnomad EAS AF: 0.0385

Gnomad SAS AF: 0.0224

Gnomad FIN AF: 0.0473

Gnomad MID AF: 0.0987

Gnomad NFE AF: 0.0425

Gnomad OTH AF: 0.0690

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

GnomAD4 genome AF: 0.0624 AC: 9501 AN: 152198 Hom.: 405 Cov.: 32 AF XY: 0.0613 AC XY: 4558 AN XY: 74406

Gnomad4 AFR AF: 0.113

Gnomad4 AMR AF: 0.0429

Gnomad4 ASJ AF: 0.0714

Gnomad4 EAS AF: 0.0386

Gnomad4 SAS AF: 0.0224

Gnomad4 FIN AF: 0.0473

Gnomad4 NFE AF: 0.0425

Gnomad4 OTH AF: 0.0682

Alfa AF: 0.0476 Hom.: 29

Bravo AF: 0.0643

Asia WGS AF: 0.0360 AC: 124 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.069
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10497176; hg19: chr2-156923420;