4-122934358-T-C

Variant names:

Variant summary

Our verdict is Benign. The variant received -19 ACMG points: 1P and 20B. PP2BP4_StrongBP6_Very_StrongBS1BS2

The NM_145207.3(AFG2A):c.767T>C(p.Ile256Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0128 in 1,614,192 control chromosomes in the GnomAD database, including 179 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. I256V) has been classified as Likely benign.

Frequency

Genomes: 𝑓 0.0091 ( 9 hom., cov: 32)

Exomes 𝑓: 0.013 ( 170 hom. )

Consequence

AFG2A
NM_145207.3 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:5

Conservation

PhyloP100: -1.30

Variant links:

Genes affected

AFG2A (HGNC:18119): (AFG2 AAA ATPase homolog A) This gene encodes a member of the ATPase associated with diverse activities family, whose members are defined by a highly conserved ATPase domain. Members of this family participate in diverse cellular processes that include membrane fusion, DNA replication, microtubule severing, and protein degradation. The protein encoded by this gene has a putative mitochondrial targeting sequence and has been proposed to function in maintenance of mitochondrial function and integrity during mouse spermatogenesis. Allelic variants in this gene have been associated with epilepsy, hearing loss, and cognitive disability syndrome. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2016]

AFG2A links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -19 ACMG points.

PP2

Missense variant in the gene, where a lot of missense mutations are associated with disease in ClinVar. The gene has 22 curated pathogenic missense variants (we use a threshold of 10). The gene has 7 curated benign missense variants. Gene score misZ: 0.46019 (below the threshold of 3.09). Trascript score misZ: 1.2041 (below the threshold of 3.09). GenCC associations: The gene is linked to microcephaly-intellectual disability-sensorineural hearing loss-epilepsy-abnormal muscle tone syndrome.

BP4

Computational evidence support a benign effect (MetaRNN=0.0034609437).

BP6

Variant 4-122934358-T-C is Benign according to our data. Variant chr4-122934358-T-C is described in ClinVar as [Benign]. Clinvar id is 475734.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr4-122934358-T-C is described in Lovd as [Benign].

BS1

Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.00909 (1385/152304) while in subpopulation NFE AF = 0.0139 (948/68030). AF 95% confidence interval is 0.0132. There are 9 homozygotes in GnomAd4. There are 629 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position FAILED quality control check.

BS2

High Homozygotes in GnomAd4 at 9 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AFG2A	NM_145207.3 link	c.767T>C	p.Ile256Thr	missense_variant	Exon 5 of 16	ENST00000274008.5	NP_660208.2	Q8NB90-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SPATA5	ENST00000274008.5 link	c.767T>C	p.Ile256Thr	missense_variant	Exon 5 of 16	1	NM_145207.3	ENSP00000274008.3		Q8NB90-1

Frequencies

GnomAD3 genomes

AF:

0.00910

AC:

1385

AN:

152186

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00360

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00982

Gnomad ASJ

AF:

0.0231

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000621

Gnomad FIN

AF:

0.00264

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.0139

Gnomad OTH

AF:

0.0124

GnomAD2 exomes

AF:

0.00916

AC:

2302

AN:

251406

AF XY:

0.00914

show subpopulations

Gnomad AFR exome

AF:

0.00369

Gnomad AMR exome

AF:

0.00584

Gnomad ASJ exome

AF:

0.0233

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00407

Gnomad NFE exome

AF:

0.0140

Gnomad OTH exome

AF:

0.0116

GnomAD4 exome

AF:

0.0131

AC:

19204

AN:

1461888

Hom.:

170

Cov.:

AF XY:

0.0126

AC XY:

9199

AN XY:

727248

show subpopulations

Gnomad4 AFR exome

AF:

0.00284

AC:

AN:

33480

Gnomad4 AMR exome

AF:

0.00682

AC:

305

AN:

44724

Gnomad4 ASJ exome

AF:

0.0246

AC:

644

AN:

26136

Gnomad4 EAS exome

AF:

0.0000252

AC:

AN:

39700

Gnomad4 SAS exome

AF:

0.00143

AC:

123

AN:

86258

Gnomad4 FIN exome

AF:

0.00489

AC:

261

AN:

53420

Gnomad4 NFE exome

AF:

0.0153

AC:

16984

AN:

1112006

Gnomad4 Remaining exome

AF:

0.0129

AC:

779

AN:

60396

Heterozygous variant carriers

1234

2468

3702

4936

6170

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Exome Het

Exome Hom

Variant carriers

664

1328

1992

2656

3320

<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:

0.00909

AC:

1385

AN:

152304

Hom.:

Cov.:

AF XY:

0.00845

AC XY:

629

AN XY:

74472

show subpopulations

Gnomad4 AFR

AF:

0.00359

AC:

0.00358552

AN:

0.00358552

Gnomad4 AMR

AF:

0.00980

AC:

0.00980264

AN:

0.00980264

Gnomad4 ASJ

AF:

0.0231

AC:

0.0230548

AN:

0.0230548

Gnomad4 EAS

AF:

0.00

AC:

AN:

Gnomad4 SAS

AF:

0.000622

AC:

0.000621891

AN:

0.000621891

Gnomad4 FIN

AF:

0.00264

AC:

0.00263852

AN:

0.00263852

Gnomad4 NFE

AF:

0.0139

AC:

0.013935

AN:

0.013935

Gnomad4 OTH

AF:

0.0123

AC:

0.0122873

AN:

0.0122873

Heterozygous variant carriers

134

200

267

334

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Genome Het

Genome Hom

Variant carriers

100

<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:

0.0131

Hom.:

Bravo

AF:

0.00920

TwinsUK

AF:

0.0170

AC:

ALSPAC

AF:

0.0145

AC:

ESP6500AA

AF:

0.00431

AC:

ESP6500EA

AF:

0.0159

AC:

137

ExAC

AF:

0.00916

AC:

1112

Asia WGS

AF:

0.00115

AC:

AN:

3478

EpiCase

AF:

0.0143

EpiControl

AF:

0.0143

ClinVar

Significance: Benign

Submissions summary: Benign:5

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Aug 06, 2018

GeneDx

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

May 01, 2024

CeGaT Center for Human Genetics Tuebingen

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

AFG2A: BP4, BS1, BS2 -

not specified

Benign:1

Jul 31, 2024

Athena Diagnostics

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

AFG2A-related disorder

Benign:1

Mar 08, 2019

PreventionGenetics, part of Exact Sciences

Significance:Benign

Review Status:no assertion criteria provided

Collection Method:clinical testing

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Microcephaly-intellectual disability-sensorineural hearing loss-epilepsy-abnormal muscle tone syndrome

Benign:1

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.051

BayesDel_addAF

Benign

-0.51

BayesDel_noAF

Benign

-0.49

CADD

Benign

0.37

DANN

Benign

0.41

DEOGEN2

Benign

0.010

Eigen

Benign

-1.4

Eigen_PC

Benign

-1.4

FATHMM_MKL

Benign

0.12

LIST_S2

Benign

0.44

MetaRNN

Benign

0.0035

MetaSVM

Benign

-0.66

PrimateAI

Benign

0.27

PROVEAN

Benign

-0.58

REVEL

Benign

0.16

Sift

Benign

1.0

Sift4G

Benign

0.44

Polyphen

0.0

Vest4

0.040

MVP

0.34

MPC

0.18

ClinPred

0.0037

GERP RS

-5.6

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Varity_R

0.031

gMVP

0.17

Mutation Taster

=98/2

polymorphism

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