16-79598581-GGT-G

Variant names:

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

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+203delAC variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.129 in 1,382,978 control chromosomes in the GnomAD database, including 2,291 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.13 (1256 hom., cov: 0)
  • Exomes 𝑓: 0.13 (1035 hom.)
• Consequence: MAF NM_005360.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.778
• 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-GGT-G is Benign according to our data. Variant chr16-79598581-GGT-G is described in ClinVar as [Benign]. Clinvar id is 1180410.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.352 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+203delAC		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+203delAC		intron_variant	Intron 1 of 1	1	NM_005360.5	ENSP00000327048.4
MAF	ENST00000393350.1	c.*198_*199delAC		3_prime_UTR_variant	Exon 1 of 1	6		ENSP00000377019.1
MAF	ENST00000569649.1	c.1118+202_1118+203delAC		intron_variant	Intron 1 of 1	5		ENSP00000455097.1

Frequencies

GnomAD3 genomes AF: 0.128 AC: 17581 AN: 137042 Hom.: 1255 Cov.: 0

Gnomad AFR AF: 0.101

Gnomad AMI AF: 0.129

Gnomad AMR AF: 0.127

Gnomad ASJ AF: 0.177

Gnomad EAS AF: 0.366

Gnomad SAS AF: 0.133

Gnomad FIN AF: 0.0885

Gnomad MID AF: 0.100

Gnomad NFE AF: 0.130

Gnomad OTH AF: 0.131

GnomAD4 exome AF: 0.129 AC: 160262 AN: 1245848 Hom.: 1035 AF XY: 0.129 AC XY: 78098 AN XY: 605650

African (AFR) AF: 0.108 AC: 3113 AN: 28782

American (AMR) AF: 0.0984 AC: 2868 AN: 29142

Ashkenazi Jewish (ASJ) AF: 0.171 AC: 3393 AN: 19880

East Asian (EAS) AF: 0.290 AC: 9590 AN: 33110

South Asian (SAS) AF: 0.127 AC: 8331 AN: 65650

European-Finnish (FIN) AF: 0.0993 AC: 2771 AN: 27914

Middle Eastern (MID) AF: 0.126 AC: 447 AN: 3560

European-Non Finnish (NFE) AF: 0.125 AC: 122784 AN: 985928

Other (OTH) AF: 0.134 AC: 6965 AN: 51882

GnomAD4 genome AF: 0.128 AC: 17586 AN: 137130 Hom.: 1256 Cov.: 0 AF XY: 0.128 AC XY: 8422 AN XY: 65816

African (AFR) AF: 0.101 AC: 3642 AN: 36102

American (AMR) AF: 0.127 AC: 1747 AN: 13772

Ashkenazi Jewish (ASJ) AF: 0.177 AC: 589 AN: 3336

East Asian (EAS) AF: 0.367 AC: 1656 AN: 4512

South Asian (SAS) AF: 0.133 AC: 522 AN: 3936

European-Finnish (FIN) AF: 0.0885 AC: 736 AN: 8314

Middle Eastern (MID) AF: 0.100 AC: 27 AN: 270

European-Non Finnish (NFE) AF: 0.130 AC: 8314 AN: 64172

Other (OTH) AF: 0.130 AC: 241 AN: 1848

Alfa AF: 0.104 Hom.: 370

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Aug 18, 2019

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.78
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs5818250; hg19: chr16-79632478;