rs10497172

Variant names:

• chr2-156113785-T-C
• rs10497172
• ENST00000428651.2:n.160-89209A>G

Variant summary

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

The ENST00000637665.1(LINC01876):​n.139-89178A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0301 in 152,330 control chromosomes in the GnomAD database, including 92 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 0.030 (92 hom., cov: 32)
• Consequence: LINC01876 ENST00000637665.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.98

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=-0.82).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0301 (4585/152330) while in subpopulation NFE AF= 0.047 (3197/68028). AF 95% confidence interval is 0.0456. There are 92 homozygotes in gnomad4. There are 2103 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 92 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01876	NR_110249.2	n.155-89209A>G		intron_variant	Intron 1 of 3
LINC01876	NR_110250.2	n.155-89178A>G		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01876	ENST00000428651.2	n.160-89209A>G		intron_variant	Intron 1 of 3	5
LINC01876	ENST00000635799.1	n.153-89209A>G		intron_variant	Intron 1 of 4	5
LINC01876	ENST00000636956.1	n.269-89178A>G		intron_variant	Intron 3 of 5	5

Frequencies

GnomAD3 genomes AF: 0.0301 AC: 4584 AN: 152212 Hom.: 92 Cov.: 32

Gnomad AFR AF: 0.00753

Gnomad AMI AF: 0.0242

Gnomad AMR AF: 0.0422

Gnomad ASJ AF: 0.0337

Gnomad EAS AF: 0.000769

Gnomad SAS AF: 0.0196

Gnomad FIN AF: 0.00943

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0470

Gnomad OTH AF: 0.0392

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

GnomAD4 genome AF: 0.0301 AC: 4585 AN: 152330 Hom.: 92 Cov.: 32 AF XY: 0.0282 AC XY: 2103 AN XY: 74492

Gnomad4 AFR AF: 0.00750

Gnomad4 AMR AF: 0.0422

Gnomad4 ASJ AF: 0.0337

Gnomad4 EAS AF: 0.000771

Gnomad4 SAS AF: 0.0199

Gnomad4 FIN AF: 0.00943

Gnomad4 NFE AF: 0.0470

Gnomad4 OTH AF: 0.0388

Alfa AF: 0.0457 Hom.: 251

Bravo AF: 0.0314

Asia WGS AF: 0.00779 AC: 28 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.0
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10497172; hg19: chr2-156970297;