Variant chr3-160226325-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_001168214.2(C3orf80):c.690A>G(p.Arg230=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00197 in 1,504,420 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0018 ( 0 hom., cov: 32)

Exomes 𝑓: 0.0020 ( 7 hom. )

Consequence

C3orf80
NM_001168214.2 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.408

Variant links:

Genes affected

C3orf80 (HGNC:40048): (chromosome 3 open reading frame 80) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

C3orf80 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=-0.71).

BP6

Variant 3-160226325-A-G is Benign according to our data. Variant chr3-160226325-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 2654257.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=0.408 with no splicing effect.

BS2

High Homozygotes in GnomAdExome4 at 7 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
C3orf80	NM_001168214.2 linkuse as main transcript	c.690A>G	p.Arg230=	synonymous_variant	1/1	ENST00000326474.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
C3orf80	ENST00000326474.5 linkuse as main transcript	c.690A>G	p.Arg230=	synonymous_variant	1/1		NM_001168214.2	P1
C3orf80	ENST00000490320.2 linkuse as main transcript	c.531A>G	p.Arg177=	synonymous_variant, NMD_transcript_variant	1/2	3

Frequencies

GnomAD3 genomes

AF:

0.00181

AC:

274

AN:

151706

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000630

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000328

Gnomad ASJ

AF:

0.000288

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00293

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00306

Gnomad OTH

AF:

0.00144

GnomAD3 exomes

AF:

0.00122

AC:

125

AN:

102714

Hom.:

AF XY:

0.00127

AC XY:

AN XY:

56628

show subpopulations

Gnomad AFR exome

AF:

0.000310

Gnomad AMR exome

AF:

0.000197

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00235

Gnomad NFE exome

AF:

0.00274

Gnomad OTH exome

AF:

0.000972

GnomAD4 exome

AF:

0.00199

AC:

2697

AN:

1352596

Hom.:

Cov.:

AF XY:

0.00195

AC XY:

1297

AN XY:

665996

show subpopulations

Gnomad4 AFR exome

AF:

0.000177

Gnomad4 AMR exome

AF:

0.000307

Gnomad4 ASJ exome

AF:

0.0000419

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00247

Gnomad4 NFE exome

AF:

0.00236

Gnomad4 OTH exome

AF:

0.00149

GnomAD4 genome

AF:

0.00180

AC:

273

AN:

151824

Hom.:

Cov.:

AF XY:

0.00189

AC XY:

140

AN XY:

74214

show subpopulations

Gnomad4 AFR

AF:

0.000629

Gnomad4 AMR

AF:

0.000327

Gnomad4 ASJ

AF:

0.000288

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00293

Gnomad4 NFE

AF:

0.00305

Gnomad4 OTH

AF:

0.00142

Alfa

AF:

0.00183

Hom.:

Bravo

AF:

0.00158

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

Mar 01, 2022

C3orf80: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.71

CADD

Benign

DANN

Benign

0.58

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