16-79598581-G-GGT

Variant names:

• chr16-79598581-G-GGT
• rs5818250
• NM_005360.5:c.1118+202_1118+203dupAC

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_005360.5(MAF):​c.1118+202_1118+203dupAC variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.37 (9690 hom., cov: 0)
  • Exomes 𝑓: 0.33 (2600 hom.)
  • Failed GnomAD Quality Control
• Consequence: MAF NM_005360.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.149
• Publications: 4 publications found

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

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP6: Variant 16-79598581-G-GGT is Benign according to our data. Variant chr16-79598581-G-GGT is described in ClinVar as [Benign]. Clinvar id is 1234541.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.401 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MAF	NM_005360.5	c.1118+202_1118+203dupAC		intron_variant	Intron 1 of 1	ENST00000326043.5	NP_005351.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MAF	ENST00000326043.5	c.1118+202_1118+203dupAC		intron_variant	Intron 1 of 1	1	NM_005360.5	ENSP00000327048.4
MAF	ENST00000393350.1	c.*198_*199dupAC		3_prime_UTR_variant	Exon 1 of 1	6		ENSP00000377019.1
MAF	ENST00000569649.1	c.1118+202_1118+203dupAC		intron_variant	Intron 1 of 1	5		ENSP00000455097.1

Frequencies

GnomAD3 genomes AF: 0.375 AC: 51294 AN: 136850 Hom.: 9692 Cov.: 0

Gnomad AFR AF: 0.355

Gnomad AMI AF: 0.391

Gnomad AMR AF: 0.392

Gnomad ASJ AF: 0.306

Gnomad EAS AF: 0.0770

Gnomad SAS AF: 0.369

Gnomad FIN AF: 0.389

Gnomad MID AF: 0.366

Gnomad NFE AF: 0.405

Gnomad OTH AF: 0.378

GnomAD4 exome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.334 AC: 413573 AN: 1237440 Hom.: 2600 Cov.: 4 AF XY: 0.334 AC XY: 200916 AN XY: 601452

African (AFR) AF: 0.314 AC: 8987 AN: 28656

American (AMR) AF: 0.351 AC: 10059 AN: 28628

Ashkenazi Jewish (ASJ) AF: 0.275 AC: 5337 AN: 19390

East Asian (EAS) AF: 0.132 AC: 4080 AN: 30946

South Asian (SAS) AF: 0.317 AC: 20563 AN: 64848

European-Finnish (FIN) AF: 0.354 AC: 9927 AN: 28038

Middle Eastern (MID) AF: 0.349 AC: 1216 AN: 3488

European-Non Finnish (NFE) AF: 0.343 AC: 336607 AN: 981976

Other (OTH) AF: 0.326 AC: 16797 AN: 51470

GnomAD4 genome AF: 0.375 AC: 51297 AN: 136938 Hom.: 9690 Cov.: 0 AF XY: 0.371 AC XY: 24383 AN XY: 65718

African (AFR) AF: 0.355 AC: 12788 AN: 36046

American (AMR) AF: 0.391 AC: 5382 AN: 13758

Ashkenazi Jewish (ASJ) AF: 0.306 AC: 1018 AN: 3328

East Asian (EAS) AF: 0.0774 AC: 349 AN: 4508

South Asian (SAS) AF: 0.367 AC: 1446 AN: 3936

European-Finnish (FIN) AF: 0.389 AC: 3225 AN: 8288

Middle Eastern (MID) AF: 0.378 AC: 102 AN: 270

European-Non Finnish (NFE) AF: 0.405 AC: 25956 AN: 64090

Other (OTH) AF: 0.374 AC: 692 AN: 1848

Alfa AF: 0.347 Hom.: 370

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Aug 15, 2019

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.15
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs5818250; hg19: chr16-79632478; COSMIC: COSV58154679; COSMIC: COSV58154679;