Variant 7-48046480-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001100159.3(C7orf57):c.371C>T(p.Pro124Leu) variant causes a missense change. The variant allele was found at a frequency of 0.9 in 1,613,174 control chromosomes in the GnomAD database, including 656,402 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 0.86 ( 56701 hom., cov: 31)

Exomes 𝑓: 0.90 ( 599701 hom. )

Consequence

C7orf57
NM_001100159.3 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 4.91

Variant links:

Genes affected

C7orf57 (HGNC:22247): (chromosome 7 open reading frame 57)

C7orf57 links:

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 (MetaRNN=2.7126152E-6).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.92 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
C7orf57	NM_001100159.3 linkuse as main transcript	c.371C>T	p.Pro124Leu	missense_variant	5/9	ENST00000348904.4	NP_001093629.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
C7orf57	ENST00000348904.4 linkuse as main transcript	c.371C>T	p.Pro124Leu	missense_variant	5/9	1	NM_001100159.3	ENSP00000335500	P1	Q8NEG2-1

Frequencies

GnomAD3 genomes

AF:

0.859

AC:

130684

AN:

152062

Hom.:

56677

Cov.:

show subpopulations

Gnomad AFR

AF:

0.749

Gnomad AMI

AF:

0.996

Gnomad AMR

AF:

0.870

Gnomad ASJ

AF:

0.841

Gnomad EAS

AF:

0.729

Gnomad SAS

AF:

0.813

Gnomad FIN

AF:

0.922

Gnomad MID

AF:

0.905

Gnomad NFE

AF:

0.926

Gnomad OTH

AF:

0.873

GnomAD3 exomes

AF:

0.872

AC:

216342

AN:

248034

Hom.:

94978

AF XY:

0.874

AC XY:

117695

AN XY:

134612

show subpopulations

Gnomad AFR exome

AF:

0.744

Gnomad AMR exome

AF:

0.852

Gnomad ASJ exome

AF:

0.846

Gnomad EAS exome

AF:

0.730

Gnomad SAS exome

AF:

0.822

Gnomad FIN exome

AF:

0.917

Gnomad NFE exome

AF:

0.925

Gnomad OTH exome

AF:

0.888

GnomAD4 exome

AF:

0.904

AC:

1321229

AN:

1460994

Hom.:

599701

Cov.:

AF XY:

0.903

AC XY:

656035

AN XY:

726732

show subpopulations

Gnomad4 AFR exome

AF:

0.745

Gnomad4 AMR exome

AF:

0.857

Gnomad4 ASJ exome

AF:

0.845

Gnomad4 EAS exome

AF:

0.690

Gnomad4 SAS exome

AF:

0.819

Gnomad4 FIN exome

AF:

0.919

Gnomad4 NFE exome

AF:

0.927

Gnomad4 OTH exome

AF:

0.890

GnomAD4 genome

AF:

0.859

AC:

130752

AN:

152180

Hom.:

56701

Cov.:

AF XY:

0.858

AC XY:

63803

AN XY:

74390

show subpopulations

Gnomad4 AFR

AF:

0.749

Gnomad4 AMR

AF:

0.870

Gnomad4 ASJ

AF:

0.841

Gnomad4 EAS

AF:

0.729

Gnomad4 SAS

AF:

0.813

Gnomad4 FIN

AF:

0.922

Gnomad4 NFE

AF:

0.926

Gnomad4 OTH

AF:

0.868

Alfa

AF:

0.905

Hom.:

154412

Bravo

AF:

0.852

TwinsUK

AF:

0.923

AC:

3422

ALSPAC

AF:

0.928

AC:

3576

ESP6500AA

AF:

0.765

AC:

3169

ESP6500EA

AF:

0.929

AC:

7793

ExAC

AF:

0.870

AC:

105232

Asia WGS

AF:

0.766

AC:

2663

AN:

3478

EpiCase

AF:

0.924

EpiControl

AF:

0.924

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Pathogenic

0.62

BayesDel_addAF

Benign

-0.39

BayesDel_noAF

Benign

-0.20

CADD

Uncertain

DANN

Uncertain

1.0

DEOGEN2

Benign

0.39

T;.;.;.;T

Eigen

Uncertain

0.51

Eigen_PC

Uncertain

0.54

FATHMM_MKL

Benign

0.67

LIST_S2

Benign

0.75

T;T;T;T;T

MetaRNN

Benign

0.0000027

T;T;T;T;T

MetaSVM

Benign

-1.1

MutationAssessor

Uncertain

2.7

.;.;.;.;M

MutationTaster

Benign

1.7e-8

P;P;P;P;P

PROVEAN

Pathogenic

-8.4

D;.;D;D;D

REVEL

Benign

0.18

Sift

Benign

0.075

T;.;T;T;T

Sift4G

Uncertain

0.042

D;T;T;D;D

Polyphen

0.86

.;.;.;.;P

Vest4

0.54

MPC

0.21

ClinPred

0.067

GERP RS

5.3

Varity_R

0.44

gMVP

0.54

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over