Variant chr3-14704350-G-A details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_032137.5(C3orf20):c.892G>A(p.Ala298Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.407 in 1,613,286 control chromosomes in the GnomAD database, including 135,711 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.41 ( 12938 hom., cov: 31)

Exomes 𝑓: 0.41 ( 122773 hom. )

Consequence

C3orf20
NM_032137.5 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.327

Variant links:

Genes affected

C3orf20 (HGNC:25320): (chromosome 3 open reading frame 20) Located in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

C3orf20 links:

C3orf20 (HGNC:):

C3orf20 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=1.2806058E-4).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.431 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
C3orf20	NM_032137.5 linkuse as main transcript	c.892G>A	p.Ala298Thr	missense_variant	7/17	ENST00000253697.8	NP_115513.4	Q8ND61-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
C3orf20	ENST00000253697.8 linkuse as main transcript	c.892G>A	p.Ala298Thr	missense_variant	7/17	1	NM_032137.5	ENSP00000253697.3	Q8ND61-1
C3orf20	ENST00000412910.1 linkuse as main transcript	c.526G>A	p.Ala176Thr	missense_variant	7/17	1		ENSP00000396081.1	Q8ND61-2
C3orf20	ENST00000435614.5 linkuse as main transcript	c.526G>A	p.Ala176Thr	missense_variant	7/17	1		ENSP00000402933.1	Q8ND61-2
C3orf20	ENST00000495387.1 linkuse as main transcript	n.-5G>A		upstream_gene_variant		3

Frequencies

GnomAD3 genomes

AF:

0.410

AC:

62156

AN:

151740

Hom.:

12924

Cov.:

show subpopulations

Gnomad AFR

AF:

0.431

Gnomad AMI

AF:

0.315

Gnomad AMR

AF:

0.439

Gnomad ASJ

AF:

0.514

Gnomad EAS

AF:

0.336

Gnomad SAS

AF:

0.308

Gnomad FIN

AF:

0.299

Gnomad MID

AF:

0.456

Gnomad NFE

AF:

0.415

Gnomad OTH

AF:

0.434

GnomAD3 exomes

AF:

0.394

AC:

98933

AN:

250808

Hom.:

20094

AF XY:

0.389

AC XY:

52789

AN XY:

135626

show subpopulations

Gnomad AFR exome

AF:

0.430

Gnomad AMR exome

AF:

0.444

Gnomad ASJ exome

AF:

0.510

Gnomad EAS exome

AF:

0.337

Gnomad SAS exome

AF:

0.312

Gnomad FIN exome

AF:

0.304

Gnomad NFE exome

AF:

0.411

Gnomad OTH exome

AF:

0.418

GnomAD4 exome

AF:

0.407

AC:

594718

AN:

1461428

Hom.:

122773

Cov.:

AF XY:

0.404

AC XY:

293643

AN XY:

727028

show subpopulations

Gnomad4 AFR exome

AF:

0.430

Gnomad4 AMR exome

AF:

0.446

Gnomad4 ASJ exome

AF:

0.511

Gnomad4 EAS exome

AF:

0.327

Gnomad4 SAS exome

AF:

0.317

Gnomad4 FIN exome

AF:

0.310

Gnomad4 NFE exome

AF:

0.416

Gnomad4 OTH exome

AF:

0.423

GnomAD4 genome

AF:

0.410

AC:

62203

AN:

151858

Hom.:

12938

Cov.:

AF XY:

0.403

AC XY:

29897

AN XY:

74224

show subpopulations

Gnomad4 AFR

AF:

0.431

Gnomad4 AMR

AF:

0.440

Gnomad4 ASJ

AF:

0.514

Gnomad4 EAS

AF:

0.336

Gnomad4 SAS

AF:

0.307

Gnomad4 FIN

AF:

0.299

Gnomad4 NFE

AF:

0.415

Gnomad4 OTH

AF:

0.436

Alfa

AF:

0.423

Hom.:

20801

Bravo

AF:

0.424

TwinsUK

AF:

0.414

AC:

1535

ALSPAC

AF:

0.415

AC:

1599

ESP6500AA

AF:

0.431

AC:

1898

ESP6500EA

AF:

0.425

AC:

3657

ExAC

AF:

0.392

AC:

47597

Asia WGS

AF:

0.339

AC:

1177

AN:

3478

EpiCase

AF:

0.425

EpiControl

AF:

0.424

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.088

BayesDel_addAF

Benign

-0.86

BayesDel_noAF

Benign

-0.86

CADD

Benign

0.13

DANN

Benign

0.42

DEOGEN2

Benign

0.0034

T;.;.

Eigen

Benign

-1.4

Eigen_PC

Benign

-1.4

FATHMM_MKL

Benign

0.0079

LIST_S2

Benign

0.59

T;.;T

MetaRNN

Benign

0.00013

T;T;T

MetaSVM

Benign

-0.92

MutationAssessor

Benign

1.2

L;.;.

PROVEAN

Benign

0.35

N;N;N

REVEL

Benign

0.028

Sift

Benign

0.43

T;T;T

Sift4G

Benign

0.32

T;T;T

Polyphen

0.017

B;.;.

Vest4

0.014

MPC

0.087

ClinPred

0.0010

GERP RS

-3.0

Varity_R

0.020

gMVP

0.18

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over