rs878873480

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_005360.5(MAF):​c.293C>T​(p.Pro98Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,458,202 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 30)
Exomes 𝑓: 0.0000014 ( 0 hom. )

Consequence

MAF
NM_005360.5 missense

Scores

2
9
8

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.77
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
MAFNM_005360.5 linkc.293C>T p.Pro98Leu missense_variant Exon 1 of 2 ENST00000326043.5 NP_005351.2 O75444-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
MAFENST00000326043.5 linkc.293C>T p.Pro98Leu missense_variant Exon 1 of 2 1 NM_005360.5 ENSP00000327048.4 O75444-1
MAFENST00000569649.1 linkc.293C>T p.Pro98Leu missense_variant Exon 1 of 2 5 ENSP00000455097.1 H3BP11
MAFENST00000393350.1 linkc.293C>T p.Pro98Leu missense_variant Exon 1 of 1 6 ENSP00000377019.1 O75444-2

Frequencies

GnomAD3 genomes
Cov.:
30
GnomAD4 exome
AF:
0.00000137
AC:
2
AN:
1458202
Hom.:
0
Cov.:
36
AF XY:
0.00000138
AC XY:
1
AN XY:
725196
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000180
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
30

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
0.49
BayesDel_addAF
Uncertain
0.022
T
BayesDel_noAF
Benign
-0.21
CADD
Uncertain
26
DANN
Benign
0.97
DEOGEN2
Uncertain
0.62
.;.;D
Eigen
Uncertain
0.24
Eigen_PC
Uncertain
0.23
FATHMM_MKL
Benign
0.52
D
LIST_S2
Uncertain
0.96
D;D;D
M_CAP
Pathogenic
0.89
D
MetaRNN
Uncertain
0.57
D;D;D
MetaSVM
Benign
-0.35
T
MutationAssessor
Benign
1.4
.;L;L
PrimateAI
Pathogenic
0.90
D
PROVEAN
Uncertain
-2.7
D;D;D
REVEL
Uncertain
0.52
Sift
Benign
0.14
T;T;T
Sift4G
Benign
0.34
T;T;T
Polyphen
0.99, 0.99
.;D;D
Vest4
0.39
MutPred
0.60
Gain of stability (P = 0.0197);Gain of stability (P = 0.0197);Gain of stability (P = 0.0197);
MVP
0.86
ClinPred
0.67
D
GERP RS
3.8
Varity_R
0.22
gMVP
0.77

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr16-79633507; API