Genetic Variant ACTR3C:c.-52+930A>G (chr7-150322539-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001164458.2(ACTR3C):c.-52+930A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.254 in 151,920 control chromosomes in the GnomAD database, including 5,062 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 0.25 ( 5061 hom., cov: 32)

Exomes 𝑓: 0.58 ( 1 hom. )

Consequence

ACTR3C
NM_001164458.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.638

Publications

6 publications found

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:

LRRC61 (HGNC:21704): (leucine rich repeat containing 61) Predicted to be active in cytosol. [provided by Alliance of Genome Resources, Apr 2022]

LRRC61 links:

ENSG00000293476 (HGNC:):

ENSG00000293476 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-1.04).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.402 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001164458.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
ACTR3C	NM_001164458.2	MANE Select	c.-52+930A>G	intron	N/A	NP_001157930.1
LRRC61	NM_001363434.1		c.-314-3302T>C	intron	N/A	NP_001350363.1
ACTR3C	NM_001351028.2		c.-593+930A>G	intron	N/A	NP_001337957.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
ACTR3C	ENST00000683684.1	MANE Select	c.-52+930A>G	intron	N/A	ENSP00000507618.1
ACTR3C	ENST00000478393.5	TSL:1	c.105+930A>G	intron	N/A	ENSP00000417426.1
ACTR3C	ENST00000477871.1	TSL:3	c.246+930A>G	intron	N/A	ENSP00000418635.1

Frequencies

GnomAD3 genomes

AF:

0.254

AC:

38554

AN:

151790

Hom.:

5067

Cov.:

show subpopulations

Gnomad AFR

AF:

0.225

Gnomad AMI

AF:

0.387

Gnomad AMR

AF:

0.194

Gnomad ASJ

AF:

0.329

Gnomad EAS

AF:

0.417

Gnomad SAS

AF:

0.273

Gnomad FIN

AF:

0.306

Gnomad MID

AF:

0.277

Gnomad NFE

AF:

0.258

Gnomad OTH

AF:

0.239

GnomAD4 exome

AF:

0.583

AC:

AN:

Hom.:

AF XY:

0.500

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.600

AC:

AN:

Other (OTH)

AF:

0.500

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.425

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.254

AC:

38562

AN:

151908

Hom.:

5061

Cov.:

AF XY:

0.257

AC XY:

19099

AN XY:

74212

show subpopulations

African (AFR)

AF:

0.225

AC:

9333

AN:

41452

American (AMR)

AF:

0.194

AC:

2959

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.329

AC:

1141

AN:

3466

East Asian (EAS)

AF:

0.417

AC:

2140

AN:

5136

South Asian (SAS)

AF:

0.273

AC:

1319

AN:

4824

European-Finnish (FIN)

AF:

0.306

AC:

3226

AN:

10540

Middle Eastern (MID)

AF:

0.257

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.258

AC:

17521

AN:

67904

Other (OTH)

AF:

0.237

AC:

499

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1491

2982

4472

5963

7454

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

406

812

1218

1624

2030

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.254

Hom.:

685

Bravo

AF:

0.246

Asia WGS

AF:

0.330

AC:

1148

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

2.7

(source)

DANN

Benign

0.40

PhyloP100

-0.64

PromoterAI

0.13

Neutral

(source)

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over