Variant chr16-79594493-C-T 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.1179G>A(p.Gln393=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000896 in 1,566,318 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.00078 ( 0 hom., cov: 32)

Exomes 𝑓: 0.00091 ( 0 hom. )

Consequence

MAF
NM_005360.5 synonymous

Scores

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 0.0170

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=-0.62).

BP6

Variant 16-79594493-C-T is Benign according to our data. Variant chr16-79594493-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 1168532.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-79594493-C-T is described in Lovd as [Likely_benign].

BP7

Synonymous conserved (PhyloP=0.017 with no splicing effect.

BS2

High AC in GnomAd4 at 119 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MAF	NM_005360.5 linkuse as main transcript	c.1179G>A	p.Gln393=	synonymous_variant	2/2	ENST00000326043.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MAF	ENST00000326043.5 linkuse as main transcript	c.1179G>A	p.Gln393=	synonymous_variant	2/2	1	NM_005360.5	A2	O75444-1
MAF	ENST00000393350.1 linkuse as main transcript	c.*4288G>A		3_prime_UTR_variant	1/1			A2	O75444-2
MAF	ENST00000569649.1 linkuse as main transcript	c.1118+4292G>A		intron_variant		5		P4

Frequencies

GnomAD3 genomes

AF:

0.000782

AC:

119

AN:

152078

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000242

Gnomad AMI

AF:

0.00110

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.000288

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.000189

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00151

Gnomad OTH

AF:

0.000957

GnomAD3 exomes

AF:

0.000634

AC:

116

AN:

182986

Hom.:

AF XY:

0.000589

AC XY:

AN XY:

96844

show subpopulations

Gnomad AFR exome

AF:

0.0000879

Gnomad AMR exome

AF:

0.000107

Gnomad ASJ exome

AF:

0.000883

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000289

Gnomad FIN exome

AF:

0.000353

Gnomad NFE exome

AF:

0.00117

Gnomad OTH exome

AF:

0.000804

GnomAD4 exome

AF:

0.000909

AC:

1285

AN:

1414240

Hom.:

Cov.:

AF XY:

0.000926

AC XY:

647

AN XY:

698686

show subpopulations

Gnomad4 AFR exome

AF:

0.000370

Gnomad4 AMR exome

AF:

0.000129

Gnomad4 ASJ exome

AF:

0.000706

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000398

Gnomad4 FIN exome

AF:

0.000219

Gnomad4 NFE exome

AF:

0.00107

Gnomad4 OTH exome

AF:

0.000803

GnomAD4 genome

AF:

0.000782

AC:

119

AN:

152078

Hom.:

Cov.:

AF XY:

0.000539

AC XY:

AN XY:

74278

show subpopulations

Gnomad4 AFR

AF:

0.000242

Gnomad4 AMR

AF:

0.00

Gnomad4 ASJ

AF:

0.000288

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.000189

Gnomad4 NFE

AF:

0.00151

Gnomad4 OTH

AF:

0.000957

Alfa

AF:

0.00117

Hom.:

Bravo

AF:

0.000699

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Ayme-Gripp syndrome;C1857768:Cataract 21 multiple types

Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Oct 11, 2023

- -

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Aug 01, 2023

MAF: BP4, BP7 -

MAF-related disorder

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

May 03, 2019

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

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.62

CADD

Benign

6.4

DANN

Benign

0.71

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