Variant 1-231241060-G-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_152379.4(C1orf131):c.82C>G(p.Leu28Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0974 in 1,614,004 control chromosomes in the GnomAD database, including 8,455 homozygotes. In-silico tool predicts a benign outcome for this variant. 11/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.084 ( 682 hom., cov: 33)

Exomes 𝑓: 0.099 ( 7773 hom. )

Consequence

C1orf131
NM_152379.4 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 3.14

Variant links:

Genes affected

C1orf131 (HGNC:25332): (chromosome 1 open reading frame 131) Enables RNA binding activity. Located in chromosome. [provided by Alliance of Genome Resources, Apr 2022]

C1orf131 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=9.944141E-4).

BP6

Variant 1-231241060-G-C is Benign according to our data. Variant chr1-231241060-G-C is described in ClinVar as [Benign]. Clinvar id is 1266325.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.156 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
C1orf131	NM_152379.4 linkuse as main transcript	c.82C>G	p.Leu28Val	missense_variant	1/7	ENST00000366649.7
C1orf131	NM_001300830.2 linkuse as main transcript	c.82C>G	p.Leu28Val	missense_variant	1/7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
C1orf131	ENST00000366649.7 linkuse as main transcript	c.82C>G	p.Leu28Val	missense_variant	1/7	1	NM_152379.4	P4	Q8NDD1-1

Frequencies

GnomAD3 genomes

AF:

0.0844

AC:

12846

AN:

152200

Hom.:

683

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0471

Gnomad AMI

AF:

0.0800

Gnomad AMR

AF:

0.161

Gnomad ASJ

AF:

0.0818

Gnomad EAS

AF:

0.0897

Gnomad SAS

AF:

0.115

Gnomad FIN

AF:

0.0530

Gnomad MID

AF:

0.0823

Gnomad NFE

AF:

0.0927

Gnomad OTH

AF:

0.0759

GnomAD3 exomes

AF:

0.107

AC:

26824

AN:

251406

Hom.:

1834

AF XY:

0.105

AC XY:

14224

AN XY:

135878

show subpopulations

Gnomad AFR exome

AF:

0.0447

Gnomad AMR exome

AF:

0.220

Gnomad ASJ exome

AF:

0.0807

Gnomad EAS exome

AF:

0.0798

Gnomad SAS exome

AF:

0.121

Gnomad FIN exome

AF:

0.0570

Gnomad NFE exome

AF:

0.0935

Gnomad OTH exome

AF:

0.101

GnomAD4 exome

AF:

0.0987

AC:

144287

AN:

1461686

Hom.:

7773

Cov.:

AF XY:

0.0987

AC XY:

71805

AN XY:

727156

show subpopulations

Gnomad4 AFR exome

AF:

0.0417

Gnomad4 AMR exome

AF:

0.214

Gnomad4 ASJ exome

AF:

0.0770

Gnomad4 EAS exome

AF:

0.0942

Gnomad4 SAS exome

AF:

0.121

Gnomad4 FIN exome

AF:

0.0567

Gnomad4 NFE exome

AF:

0.0974

Gnomad4 OTH exome

AF:

0.0902

GnomAD4 genome

AF:

0.0844

AC:

12849

AN:

152318

Hom.:

682

Cov.:

AF XY:

0.0837

AC XY:

6237

AN XY:

74492

show subpopulations

Gnomad4 AFR

AF:

0.0470

Gnomad4 AMR

AF:

0.161

Gnomad4 ASJ

AF:

0.0818

Gnomad4 EAS

AF:

0.0899

Gnomad4 SAS

AF:

0.116

Gnomad4 FIN

AF:

0.0530

Gnomad4 NFE

AF:

0.0927

Gnomad4 OTH

AF:

0.0751

Alfa

AF:

0.0819

Hom.:

484

Bravo

AF:

0.0890

TwinsUK

AF:

0.0947

AC:

351

ALSPAC

AF:

0.102

AC:

394

ESP6500AA

AF:

0.0477

AC:

210

ESP6500EA

AF:

0.103

AC:

888

ExAC

AF:

0.102

AC:

12432

Asia WGS

AF:

0.100

AC:

350

AN:

3478

EpiCase

AF:

0.0947

EpiControl

AF:

0.0928

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 30, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.079

BayesDel_addAF

Benign

-0.67

BayesDel_noAF

Benign

-0.59

CADD

Benign

DANN

Uncertain

0.99

DEOGEN2

Benign

0.028

T;T;.;T

Eigen

Benign

0.084

Eigen_PC

Benign

-0.11

FATHMM_MKL

Benign

0.18

LIST_S2

Benign

0.77

T;T;T;T

MetaRNN

Benign

0.00099

T;T;T;T

MetaSVM

Benign

-1.1

MutationAssessor

Uncertain

2.2

M;.;M;.

MutationTaster

Benign

1.0

P;P;P

PROVEAN

Benign

-1.6

N;N;N;N

REVEL

Benign

0.080

Sift

Uncertain

0.017

D;D;D;D

Sift4G

Benign

0.078

T;T;T;T

Polyphen

1.0

D;.;.;.

Vest4

0.14

MPC

0.26

ClinPred

0.072

GERP RS

3.1

Varity_R

0.20

gMVP

0.12

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