rs10497172

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000428651.2(LINC01876):​n.160-89209A>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 ENST00000428651.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.98
• Publications: 5 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• 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

African (AFR) AF: 0.00750 AC: 312 AN: 41578

American (AMR) AF: 0.0422 AC: 646 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0337 AC: 117 AN: 3472

East Asian (EAS) AF: 0.000771 AC: 4 AN: 5190

South Asian (SAS) AF: 0.0199 AC: 96 AN: 4832

European-Finnish (FIN) AF: 0.00943 AC: 100 AN: 10610

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0470 AC: 3197 AN: 68028

Other (OTH) AF: 0.0388 AC: 82 AN: 2116

Alfa AF: 0.0442 Hom.: 325

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
PhyloP100		2.0

Splicing

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

Other links and lift over

dbSNP: rs10497172; hg19: chr2-156970297;