Variant 10-126459169-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate

The NM_001350921.2(C10orf90):c.2059C>T(p.Arg687Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00408 in 1,614,124 control chromosomes in the GnomAD database, including 18 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0033 ( 0 hom., cov: 32)

Exomes 𝑓: 0.0042 ( 18 hom. )

Consequence

C10orf90
NM_001350921.2 missense

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 2.60

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]

C10orf90 links:

(HGNC:):

links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -6 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.009523243).

BP6

Variant 10-126459169-G-A is Benign according to our data. Variant chr10-126459169-G-A is described in ClinVar as [Benign]. Clinvar id is 719394.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
C10orf90	NM_001350921.2 linkuse as main transcript	c.2059C>T	p.Arg687Trp	missense_variant	7/10	ENST00000488181.3
LOC728158	NR_148989.1 linkuse as main transcript	n.1183G>A		non_coding_transcript_exon_variant	7/7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
C10orf90	ENST00000488181.3 linkuse as main transcript	c.2059C>T	p.Arg687Trp	missense_variant	7/10	2	NM_001350921.2	P2
	ENST00000656840.1 linkuse as main transcript	n.1183G>A		non_coding_transcript_exon_variant	7/7

Frequencies

GnomAD3 genomes

AF:

0.00328

AC:

499

AN:

152158

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000990

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00118

Gnomad ASJ

AF:

0.000577

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00104

Gnomad FIN

AF:

0.0117

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00445

Gnomad OTH

AF:

0.00287

GnomAD3 exomes

AF:

0.00331

AC:

833

AN:

251394

Hom.:

AF XY:

0.00339

AC XY:

460

AN XY:

135862

show subpopulations

Gnomad AFR exome

AF:

0.000492

Gnomad AMR exome

AF:

0.000781

Gnomad ASJ exome

AF:

0.000595

Gnomad EAS exome

AF:

0.0000544

Gnomad SAS exome

AF:

0.000751

Gnomad FIN exome

AF:

0.0110

Gnomad NFE exome

AF:

0.00449

Gnomad OTH exome

AF:

0.00310

GnomAD4 exome

AF:

0.00417

AC:

6089

AN:

1461848

Hom.:

Cov.:

AF XY:

0.00401

AC XY:

2917

AN XY:

727230

show subpopulations

Gnomad4 AFR exome

AF:

0.000836

Gnomad4 AMR exome

AF:

0.000738

Gnomad4 ASJ exome

AF:

0.000497

Gnomad4 EAS exome

AF:

0.000101

Gnomad4 SAS exome

AF:

0.000788

Gnomad4 FIN exome

AF:

0.0102

Gnomad4 NFE exome

AF:

0.00470

Gnomad4 OTH exome

AF:

0.00280

GnomAD4 genome

AF:

0.00328

AC:

499

AN:

152276

Hom.:

Cov.:

AF XY:

0.00351

AC XY:

261

AN XY:

74460

show subpopulations

Gnomad4 AFR

AF:

0.000987

Gnomad4 AMR

AF:

0.00118

Gnomad4 ASJ

AF:

0.000577

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00104

Gnomad4 FIN

AF:

0.0117

Gnomad4 NFE

AF:

0.00445

Gnomad4 OTH

AF:

0.00284

Alfa

AF:

0.00357

Hom.:

Bravo

AF:

0.00264

TwinsUK

AF:

0.00189

AC:

ALSPAC

AF:

0.00441

AC:

ESP6500AA

AF:

0.000681

AC:

ESP6500EA

AF:

0.00384

AC:

ExAC

AF:

0.00330

AC:

400

Asia WGS

AF:

0.000289

AC:

AN:

3478

EpiCase

AF:

0.00409

EpiControl

AF:

0.00373

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 submitter

clinical testing

Invitae

Feb 25, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Pathogenic

0.80

BayesDel_addAF

Benign

-0.0066

BayesDel_noAF

Pathogenic

0.22

Cadd

Pathogenic

Dann

Pathogenic

1.0

DEOGEN2

Benign

0.36

T;T;.

Eigen

Uncertain

0.52

Eigen_PC

Uncertain

0.46

FATHMM_MKL

Benign

0.51

LIST_S2

Uncertain

0.95

D;D;D

MetaRNN

Benign

0.0095

T;T;T

MetaSVM

Uncertain

-0.27

MutationAssessor

Pathogenic

2.9

M;.;.

MutationTaster

Benign

0.96

D;D;D;N

PROVEAN

Pathogenic

-7.6

D;D;D

REVEL

Uncertain

0.43

Sift

Pathogenic

0.0

D;D;D

Sift4G

Pathogenic

0.0

D;D;D

Polyphen

1.0

D;.;.

Vest4

0.86

MVP

0.77

MPC

0.45

ClinPred

0.055

GERP RS

4.1

Varity_R

0.72

gMVP

0.69

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over