Genetic Variant MAF:c.1118+198_1118+203delACACAC (chr16-79598581-GGTGTGT-G) – ACMG Classification: Likely_benign (-4 pts)

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BS2

The NM_005360.5(MAF):c.1118+198_1118+203delACACAC variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00357 in 1,409,968 control chromosomes in the GnomAD database, including 6 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0024 ( 0 hom., cov: 0)

Exomes 𝑓: 0.0037 ( 6 hom. )

Consequence

MAF
NM_005360.5 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.72

Publications

4 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:

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -4 ACMG points.

BS2

High Homozygotes in GnomAdExome4 at 6 AD,AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MAF	NM_005360.5 link	c.1118+198_1118+203delACACAC		intron_variant	Intron 1 of 1	ENST00000326043.5	NP_005351.2	O75444-1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
MAF	ENST00000326043.5 link	c.1118+198_1118+203delACACAC	intron_variant	Intron 1 of 1	1	NM_005360.5	ENSP00000327048.4	O75444-1
MAF	ENST00000393350.1 link	c.194_199delACACAC	3_prime_UTR_variant	Exon 1 of 1	6		ENSP00000377019.1	O75444-2
MAF	ENST00000569649.1 link	c.1118+198_1118+203delACACAC	intron_variant	Intron 1 of 1	5		ENSP00000455097.1	H3BP11

Frequencies

GnomAD3 genomes

AF:

0.00241

AC:

331

AN:

137228

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000749

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00268

Gnomad ASJ

AF:

0.00270

Gnomad EAS

AF:

0.00133

Gnomad SAS

AF:

0.00405

Gnomad FIN

AF:

0.000240

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00353

Gnomad OTH

AF:

0.00381

GnomAD4 exome

AF:

0.00370

AC:

4703

AN:

1272652

Hom.:

AF XY:

0.00374

AC XY:

2311

AN XY:

618394

show subpopulations

African (AFR)

AF:

0.00125

AC:

AN:

29492

American (AMR)

AF:

0.00224

AC:

AN:

29432

Ashkenazi Jewish (ASJ)

AF:

0.00414

AC:

AN:

20046

East Asian (EAS)

AF:

0.000937

AC:

AN:

33092

South Asian (SAS)

AF:

0.00360

AC:

240

AN:

66676

European-Finnish (FIN)

AF:

0.000489

AC:

AN:

28608

Middle Eastern (MID)

AF:

0.00139

AC:

AN:

3604

European-Non Finnish (NFE)

AF:

0.00399

AC:

4030

AN:

1008842

Other (OTH)

AF:

0.00373

AC:

197

AN:

52860

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.469

Heterozygous variant carriers

214

428

643

857

1071

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.00245

AC:

336

AN:

137316

Hom.:

Cov.:

AF XY:

0.00250

AC XY:

165

AN XY:

65918

show subpopulations

African (AFR)

AF:

0.000775

AC:

AN:

36148

American (AMR)

AF:

0.00268

AC:

AN:

13800

Ashkenazi Jewish (ASJ)

AF:

0.00270

AC:

AN:

3336

East Asian (EAS)

AF:

0.00133

AC:

AN:

4518

South Asian (SAS)

AF:

0.00406

AC:

AN:

3944

European-Finnish (FIN)

AF:

0.000240

AC:

AN:

8344

Middle Eastern (MID)

AF:

0.00

AC:

AN:

270

European-Non Finnish (NFE)

AF:

0.00355

AC:

228

AN:

64234

Other (OTH)

AF:

0.00539

AC:

AN:

1854

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.00197

Hom.:

370

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

1.7

Mutation Taster

=100/0

polymorphism

(source)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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chr16-79598581-GGTGTGT-G

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over