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GeneBe

10-126464816-G-A

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 2P and 10B. PM4BP6_ModerateBS1BS2

The NM_001350921.2(C10orf90):c.1705C>T(p.Arg569Ter) variant causes a stop gained change. The variant allele was found at a frequency of 0.0021 in 1,614,044 control chromosomes in the GnomAD database, including 63 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Variant results in nonsense mediated mRNA decay.

Frequency

Genomes: 𝑓 0.011 ( 25 hom., cov: 32)
Exomes 𝑓: 0.0011 ( 38 hom. )

Consequence

C10orf90
NM_001350921.2 stop_gained

Scores

1
3
3

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 3.77
Variant links:
Genes affected
C10orf90 (HGNC:26563): (chromosome 10 open reading frame 90) Predicted to enable histone deacetylase binding activity; microtubule binding activity; and ubiquitin protein ligase activity. Predicted to be involved in several processes, including protein stabilization; regulation of cell cycle process; and response to ionizing radiation. Located in several cellular components, including cytoskeleton; cytosol; and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

PM4
?
    PM4 - Protein length changes as a result of in-frame deletions/insertions in a nonrepeat region or stop-loss variants
Stoplost variant in NM_001350921.2 Downstream stopcodon found after 12 codons.
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 10-126464816-G-A is Benign according to our data. Variant chr10-126464816-G-A is described in ClinVar as [Benign]. Clinvar id is 709837.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
    BS1 - Allele frequency is greater than expected for disorder
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0113 (1712/152158) while in subpopulation AFR AF= 0.0378 (1570/41490). AF 95% confidence interval is 0.0363. There are 25 homozygotes in gnomad4. There are 780 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
    BS2 - Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age
High Homozygotes in GnomAd at 25 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
C10orf90NM_001350921.2 linkuse as main transcriptc.1705C>T p.Arg569Ter stop_gained 5/10 ENST00000488181.3

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
C10orf90ENST00000488181.3 linkuse as main transcriptc.1705C>T p.Arg569Ter stop_gained 5/102 NM_001350921.2 P2

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0112
AC:
1703
AN:
152040
Hom.:
25
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0378
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00688
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000416
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00633
Gnomad NFE
AF:
0.000191
Gnomad OTH
AF:
0.00907
GnomAD3 exomes
AF:
0.00296
AC:
743
AN:
251420
Hom.:
17
AF XY:
0.00207
AC XY:
281
AN XY:
135870
show subpopulations
Gnomad AFR exome
AF:
0.0399
Gnomad AMR exome
AF:
0.00182
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.000261
Gnomad FIN exome
AF:
0.0000462
Gnomad NFE exome
AF:
0.000158
Gnomad OTH exome
AF:
0.000652
GnomAD4 exome
AF:
0.00115
AC:
1675
AN:
1461886
Hom.:
38
Cov.:
32
AF XY:
0.000990
AC XY:
720
AN XY:
727244
show subpopulations
Gnomad4 AFR exome
AF:
0.0385
Gnomad4 AMR exome
AF:
0.00201
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000252
Gnomad4 SAS exome
AF:
0.000359
Gnomad4 FIN exome
AF:
0.0000187
Gnomad4 NFE exome
AF:
0.0000863
Gnomad4 OTH exome
AF:
0.00265
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0113
AC:
1712
AN:
152158
Hom.:
25
Cov.:
32
AF XY:
0.0105
AC XY:
780
AN XY:
74384
show subpopulations
Gnomad4 AFR
AF:
0.0378
Gnomad4 AMR
AF:
0.00687
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000416
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000191
Gnomad4 OTH
AF:
0.00898
Alfa
AF:
0.00149
Hom.:
6
Bravo
AF:
0.0133
TwinsUK
AF:
0.000270
AC:
1
ALSPAC
AF:
0.00
AC:
0
ESP6500AA
AF:
0.0379
AC:
167
ESP6500EA
AF:
0.000116
AC:
1
ExAC
?
    Exome Aggregation Consortium database
AF:
0.00371
AC:
450
Asia WGS
AF:
0.00202
AC:
7
AN:
3478
EpiCase
AF:
0.000273
EpiControl
AF:
0.00

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingInvitaeDec 31, 2019- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
0.0027
T
BayesDel_noAF
Pathogenic
0.26
Cadd
Pathogenic
40
Dann
Uncertain
1.0
Eigen
Uncertain
0.60
Eigen_PC
Uncertain
0.34
FATHMM_MKL
Benign
0.69
D
MutationTaster
Benign
1.0
A;A;A;N
Vest4
0.20
GERP RS
2.5

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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: rs114882604; hg19: chr10-128153385; API