Variant 16-79599201-T-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2

The NM_005360.5(MAF):c.702A>C(p.Gly234=) 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:4

Conservation

PhyloP100: -1.66

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 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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 [Likely_benign]. Clinvar id 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 AC in GnomAd4 at 1310 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MAF	NM_005360.5 linkuse as main transcript	c.702A>C	p.Gly234=	synonymous_variant	1/2	ENST00000326043.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MAF	ENST00000326043.5 linkuse as main transcript	c.702A>C	p.Gly234=	synonymous_variant	1/2	1	NM_005360.5	A2	O75444-1
MAF	ENST00000569649.1 linkuse as main transcript	c.702A>C	p.Gly234=	synonymous_variant	1/2	5		P4
MAF	ENST00000393350.1 linkuse as main transcript	c.702A>C	p.Gly234=	synonymous_variant	1/1			A2	O75444-2

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

GnomAD3 exomes

AF:

0.00439

AC:

AN:

228

Hom.:

AF XY:

0.00794

AC XY:

AN XY:

126

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

Gnomad4 AFR exome

AF:

0.00147

Gnomad4 AMR exome

AF:

0.00164

Gnomad4 ASJ exome

AF:

0.00114

Gnomad4 EAS exome

AF:

0.000493

Gnomad4 SAS exome

AF:

0.00304

Gnomad4 FIN exome

AF:

0.0254

Gnomad4 NFE exome

AF:

0.0131

Gnomad4 OTH exome

AF:

0.00938

GnomAD4 genome

AF:

0.00910

AC:

1310

AN:

143936

Hom.:

Cov.:

AF XY:

0.0102

AC XY:

715

AN XY:

69898

show subpopulations

Gnomad4 AFR

AF:

0.00188

Gnomad4 AMR

AF:

0.00323

Gnomad4 ASJ

AF:

0.00119

Gnomad4 EAS

AF:

0.000621

Gnomad4 SAS

AF:

0.00233

Gnomad4 FIN

AF:

0.0341

Gnomad4 NFE

AF:

0.0135

Gnomad4 OTH

AF:

0.00600

Alfa

AF:

0.00941

Hom.:

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Jan 04, 2021	- -
Benign, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Jul 01, 2024	MAF: BP4, BP7, BS1, BS2 -

not specified

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

Ayme-Gripp syndrome;C1857768:Cataract 21 multiple types

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Invitae

Dec 07, 2023

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.77

CADD

Benign

4.0

DANN

Benign

0.42

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