Variant rs78661149 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1

The NM_001164458.2(ACTR3C):c.361C>T(p.Gln121Ter) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0421 in 148,166 control chromosomes in the GnomAD database, including 205 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Variant results in nonsense mediated mRNA decay.

Frequency

Genomes: 𝑓 0.042 ( 205 hom., cov: 30)

Exomes 𝑓: 0.043 ( 2980 hom. )

Failed GnomAD Quality Control

Consequence

ACTR3C
NM_001164458.2 stop_gained

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.0600

Variant links:

Genes affected

ACTR3C (HGNC:37282): (actin related protein 3C) Predicted to enable ATP binding activity. Predicted to contribute to actin filament binding activity. Located in extracellular exosome. [provided by Alliance of Genome Resources, Apr 2022]

ACTR3C links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP6

Variant 7-150286477-G-A is Benign according to our data. Variant chr7-150286477-G-A is described in ClinVar as [Benign]. Clinvar id is 402338.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.072 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ACTR3C	NM_001164458.2 linkuse as main transcript	c.361C>T	p.Gln121Ter	stop_gained	5/8	ENST00000683684.1	NP_001157930.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ACTR3C	ENST00000683684.1 linkuse as main transcript	c.361C>T	p.Gln121Ter	stop_gained	5/8		NM_001164458.2	ENSP00000507618	P1	Q9C0K3-1

Frequencies

GnomAD3 genomes

AF:

0.0422

AC:

6242

AN:

148052

Hom.:

203

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0166

Gnomad AMI

AF:

0.0575

Gnomad AMR

AF:

0.0258

Gnomad ASJ

AF:

0.0696

Gnomad EAS

AF:

0.00449

Gnomad SAS

AF:

0.0783

Gnomad FIN

AF:

0.0759

Gnomad MID

AF:

0.0541

Gnomad NFE

AF:

0.0548

Gnomad OTH

AF:

0.0388

GnomAD3 exomes

AF:

0.0495

AC:

12268

AN:

247772

Hom.:

478

AF XY:

0.0533

AC XY:

7128

AN XY:

133696

show subpopulations

Gnomad AFR exome

AF:

0.0169

Gnomad AMR exome

AF:

0.0197

Gnomad ASJ exome

AF:

0.0506

Gnomad EAS exome

AF:

0.00517

Gnomad SAS exome

AF:

0.0900

Gnomad FIN exome

AF:

0.0853

Gnomad NFE exome

AF:

0.0530

Gnomad OTH exome

AF:

0.0503

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.0434

AC:

61001

AN:

1406730

Hom.:

2980

Cov.:

AF XY:

0.0455

AC XY:

31819

AN XY:

699942

show subpopulations

Gnomad4 AFR exome

AF:

0.0152

Gnomad4 AMR exome

AF:

0.0193

Gnomad4 ASJ exome

AF:

0.0517

Gnomad4 EAS exome

AF:

0.00633

Gnomad4 SAS exome

AF:

0.0940

Gnomad4 FIN exome

AF:

0.0801

Gnomad4 NFE exome

AF:

0.0404

Gnomad4 OTH exome

AF:

0.0458

GnomAD4 genome

AF:

0.0421

AC:

6244

AN:

148166

Hom.:

205

Cov.:

AF XY:

0.0430

AC XY:

3104

AN XY:

72186

show subpopulations

Gnomad4 AFR

AF:

0.0166

Gnomad4 AMR

AF:

0.0257

Gnomad4 ASJ

AF:

0.0696

Gnomad4 EAS

AF:

0.00450

Gnomad4 SAS

AF:

0.0788

Gnomad4 FIN

AF:

0.0759

Gnomad4 NFE

AF:

0.0548

Gnomad4 OTH

AF:

0.0395

Alfa

AF:

0.0588

Hom.:

ExAC

AF:

0.0558

AC:

6771

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Mar 28, 2016

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: ExAC frequency -

not provided

Benign:1

Benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.070

BayesDel_noAF

Pathogenic

0.17

CADD

Pathogenic

DANN

Benign

0.95

Eigen

Uncertain

0.21

Eigen_PC

Benign

-0.16

FATHMM_MKL

Benign

0.051

MutationTaster

Benign

1.0

A;A

Vest4

0.24, 0.23

GERP RS

1.5

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