16-79599201-T-G

Variant names:

Variant summary

Our verdict is Benign. The variant received -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2

The NM_005360.5(MAF):c.702A>C(p.Gly234Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0119 in 974,532 control chromosomes in the GnomAD database, including 82 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.0091 ( 8 hom., cov: 29)

Exomes 𝑓: 0.012 ( 74 hom. )

Consequence

MAF
NM_005360.5 synonymous

Scores

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:5

Conservation

PhyloP100: -1.66

Publications

1 publications found

Variant links:

Genes affected

MAF (HGNC:6776): (MAF bZIP transcription factor) The protein encoded by this gene is a DNA-binding, leucine zipper-containing transcription factor that acts as a homodimer or as a heterodimer. Depending on the binding site and binding partner, the encoded protein can be a transcriptional activator or repressor. This protein plays a role in the regulation of several cellular processes, including embryonic lens fiber cell development, increased T-cell susceptibility to apoptosis, and chondrocyte terminal differentiation. Defects in this gene are a cause of juvenile-onset pulverulent cataract as well as congenital cerulean cataract 4 (CCA4). Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jan 2010]

MAF Gene-Disease associations (from GenCC):

Ayme-Gripp syndrome
Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics, G2P
cataract 21 multiple types
Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: G2P, Ambry Genetics
cataract - microcornea syndrome
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
cerulean cataract
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
pulverulent cataract
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
Fine-Lubinsky syndrome
Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

MAF links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -17 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.77).

BP6

Variant 16-79599201-T-G is Benign according to our data. Variant chr16-79599201-T-G is described in ClinVar as Benign/Likely_benign. ClinVar VariationId is 259753.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-1.66 with no splicing effect.

BS2

High Homozygotes in GnomAd4 at 8 AD,AR gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005360.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAF	NM_005360.5	MANE Select	c.702A>C	p.Gly234Gly	synonymous	Exon 1 of 2	NP_005351.2
	MAF	NM_001031804.3		c.702A>C	p.Gly234Gly	synonymous	Exon 1 of 1	NP_001026974.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein
MAF	ENST00000326043.5	TSL:1 MANE Select	c.702A>C	p.Gly234Gly	synonymous	Exon 1 of 2	ENSP00000327048.4
MAF	ENST00000569649.1	TSL:5	c.702A>C	p.Gly234Gly	synonymous	Exon 1 of 2	ENSP00000455097.1
MAF	ENST00000393350.1	TSL:6	c.702A>C	p.Gly234Gly	synonymous	Exon 1 of 1	ENSP00000377019.1

Frequencies

GnomAD3 genomes

AF:

0.00910

AC:

1310

AN:

143930

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00188

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00323

Gnomad ASJ

AF:

0.00119

Gnomad EAS

AF:

0.000618

Gnomad SAS

AF:

0.00232

Gnomad FIN

AF:

0.0341

Gnomad MID

AF:

0.00333

Gnomad NFE

AF:

0.0135

Gnomad OTH

AF:

0.00604

GnomAD2 exomes

AF:

0.00439

AC:

AN:

228

AF XY:

0.00794

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00476

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.0123

AC:

10254

AN:

830596

Hom.:

Cov.:

AF XY:

0.0124

AC XY:

4752

AN XY:

384606

show subpopulations

African (AFR)

AF:

0.00147

AC:

AN:

15606

American (AMR)

AF:

0.00164

AC:

AN:

1222

Ashkenazi Jewish (ASJ)

AF:

0.00114

AC:

AN:

5286

East Asian (EAS)

AF:

0.000493

AC:

AN:

4058

South Asian (SAS)

AF:

0.00304

AC:

AN:

17114

European-Finnish (FIN)

AF:

0.0254

AC:

AN:

1180

Middle Eastern (MID)

AF:

0.00122

AC:

AN:

1640

European-Non Finnish (NFE)

AF:

0.0131

AC:

9880

AN:

757080

Other (OTH)

AF:

0.00938

AC:

257

AN:

27410

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.426

Heterozygous variant carriers

432

863

1295

1726

2158

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

496

992

1488

1984

2480

<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:

0.00910

AC:

1310

AN:

143936

Hom.:

Cov.:

AF XY:

0.0102

AC XY:

715

AN XY:

69898

show subpopulations

African (AFR)

AF:

0.00188

AC:

AN:

39878

American (AMR)

AF:

0.00323

AC:

AN:

14564

Ashkenazi Jewish (ASJ)

AF:

0.00119

AC:

AN:

3368

East Asian (EAS)

AF:

0.000621

AC:

AN:

4834

South Asian (SAS)

AF:

0.00233

AC:

AN:

4718

European-Finnish (FIN)

AF:

0.0341

AC:

276

AN:

8102

Middle Eastern (MID)

AF:

0.00365

AC:

AN:

274

European-Non Finnish (NFE)

AF:

0.0135

AC:

881

AN:

65294

Other (OTH)

AF:

0.00600

AC:

AN:

2000

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

135

203

270

338

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

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:

0.00941

Hom.:

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:5

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Jan 04, 2021

GeneDx

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

Oct 01, 2025

CeGaT Center for Human Genetics Tuebingen

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

MAF: BP4, BP7, BS1, BS2

not specified

Benign:1

PreventionGenetics, part of Exact Sciences

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

Ayme-Gripp syndrome;C1857768:Cataract 21 multiple types

Benign:1

Jan 06, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

Inborn genetic diseases

Benign:1

Jun 07, 2024

Ambry Genetics

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.77

CADD

Benign

4.0

(source)

DANN

Benign

0.42

PhyloP100

-1.7

Mutation Taster

=100/0

polymorphism

(source)

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

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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

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over