rs10497172

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.98
Variant links:
Genes affected
LINC01876 (HGNC:52695): (long intergenic non-protein coding RNA 1876)

Genome browser will be placed here

ACMG classification

Classification made for transcript

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
LINC01876NR_110249.2 linkn.155-89209A>G intron_variant Intron 1 of 3
LINC01876NR_110250.2 linkn.155-89178A>G intron_variant Intron 1 of 3

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
LINC01876ENST00000428651.2 linkn.160-89209A>G intron_variant Intron 1 of 3 5
LINC01876ENST00000635799.1 linkn.153-89209A>G intron_variant Intron 1 of 4 5
LINC01876ENST00000636956.1 linkn.269-89178A>G intron_variant Intron 3 of 5 5

Frequencies

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs10497172; hg19: chr2-156970297; API