Variant chr3-14715295-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_032137.5(C3orf20):c.1320A>G(p.Pro440=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00257 in 1,611,866 control chromosomes in the GnomAD database, including 11 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0023 ( 4 hom., cov: 33)

Exomes 𝑓: 0.0026 ( 7 hom. )

Consequence

C3orf20
NM_032137.5 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.667

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BP6

Variant 3-14715295-A-G is Benign according to our data. Variant chr3-14715295-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 2653587.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-0.667 with no splicing effect.

BS2

High Homozygotes in GnomAd4 at 4 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
C3orf20	NM_032137.5 linkuse as main transcript	c.1320A>G	p.Pro440=	synonymous_variant	9/17	ENST00000253697.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
C3orf20	ENST00000253697.8 linkuse as main transcript	c.1320A>G	p.Pro440=	synonymous_variant	9/17	1	NM_032137.5	P2	Q8ND61-1
C3orf20	ENST00000412910.1 linkuse as main transcript	c.954A>G	p.Pro318=	synonymous_variant	9/17	1		A2	Q8ND61-2
C3orf20	ENST00000435614.5 linkuse as main transcript	c.954A>G	p.Pro318=	synonymous_variant	9/17	1		A2	Q8ND61-2
C3orf20	ENST00000495387.1 linkuse as main transcript	n.424A>G		non_coding_transcript_exon_variant	3/5	3

Frequencies

GnomAD3 genomes

AF:

0.00228

AC:

347

AN:

152190

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000386

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00170

Gnomad ASJ

AF:

0.00231

Gnomad EAS

AF:

0.000193

Gnomad SAS

AF:

0.000208

Gnomad FIN

AF:

0.00734

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00315

Gnomad OTH

AF:

0.00143

GnomAD3 exomes

AF:

0.00270

AC:

676

AN:

250722

Hom.:

AF XY:

0.00252

AC XY:

342

AN XY:

135502

show subpopulations

Gnomad AFR exome

AF:

0.000246

Gnomad AMR exome

AF:

0.00134

Gnomad ASJ exome

AF:

0.00368

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.0000982

Gnomad FIN exome

AF:

0.00713

Gnomad NFE exome

AF:

0.00366

Gnomad OTH exome

AF:

0.00279

GnomAD4 exome

AF:

0.00260

AC:

3802

AN:

1459556

Hom.:

Cov.:

AF XY:

0.00259

AC XY:

1880

AN XY:

726088

show subpopulations

Gnomad4 AFR exome

AF:

0.000359

Gnomad4 AMR exome

AF:

0.00125

Gnomad4 ASJ exome

AF:

0.00383

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000209

Gnomad4 FIN exome

AF:

0.00798

Gnomad4 NFE exome

AF:

0.00276

Gnomad4 OTH exome

AF:

0.00209

GnomAD4 genome

AF:

0.00228

AC:

347

AN:

152310

Hom.:

Cov.:

AF XY:

0.00246

AC XY:

183

AN XY:

74484

show subpopulations

Gnomad4 AFR

AF:

0.000385

Gnomad4 AMR

AF:

0.00170

Gnomad4 ASJ

AF:

0.00231

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.000208

Gnomad4 FIN

AF:

0.00734

Gnomad4 NFE

AF:

0.00315

Gnomad4 OTH

AF:

0.00142

Alfa

AF:

0.00249

Hom.:

Bravo

AF:

0.00181

EpiCase

AF:

0.00274

EpiControl

AF:

0.00208

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Sep 01, 2022

C3orf20: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

2.2

DANN

Benign

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