chr2-156114540-T-G

Position:

• chr2-156114540-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NR_110249.2(LINC01876):​n.155-89964A>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 0.0305 in 152,262 control chromosomes in the GnomAD database, including 91 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 0.031 (91 hom., cov: 32)
• Consequence: LINC01876 NR_110249.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.186

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).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0305 (4647/152262) while in subpopulation NFE AF= 0.047 (3195/68008). AF 95% confidence interval is 0.0456. There are 91 homozygotes in gnomad4. There are 2132 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 91 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01876	NR_110249.2	n.155-89964A>C		intron_variant, non_coding_transcript_variant
LINC01876	NR_110250.2	n.155-89933A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01876	ENST00000635799.1	n.153-89964A>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.0305 AC: 4646 AN: 152144 Hom.: 91 Cov.: 32

Gnomad AFR AF: 0.00772

Gnomad AMI AF: 0.0231

Gnomad AMR AF: 0.0424

Gnomad ASJ AF: 0.0337

Gnomad EAS AF: 0.0102

Gnomad SAS AF: 0.0203

Gnomad FIN AF: 0.00933

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0470

Gnomad OTH AF: 0.0406

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

GnomAD4 genome AF: 0.0305 AC: 4647 AN: 152262 Hom.: 91 Cov.: 32 AF XY: 0.0286 AC XY: 2132 AN XY: 74468

Gnomad4 AFR AF: 0.00770

Gnomad4 AMR AF: 0.0424

Gnomad4 ASJ AF: 0.0337

Gnomad4 EAS AF: 0.0102

Gnomad4 SAS AF: 0.0205

Gnomad4 FIN AF: 0.00933

Gnomad4 NFE AF: 0.0470

Gnomad4 OTH AF: 0.0402

Alfa AF: 0.0408 Hom.: 30

Bravo AF: 0.0318

Asia WGS AF: 0.0150 AC: 53 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	0.91
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10497171; hg19: chr2-156971052;