chr16-79594712-G-GA

Variant names:

• chr16-79594712-G-GA
• rs36052284
• NM_005360.5:c.1119-160dupT

Variant summary

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

The NM_005360.5(MAF):​c.1119-160dupT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.351 in 1,273,678 control chromosomes in the GnomAD database, including 48,997 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.33 (8418 hom., cov: 0)
  • Exomes 𝑓: 0.35 (40579 hom.)
• Consequence: MAF NM_005360.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.442
• Publications: 1 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 16-79594712-G-GA is Benign according to our data. Variant chr16-79594712-G-GA is described in ClinVar as [Benign]. Clinvar id is 1280411.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.406 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MAF	NM_005360.5	c.1119-160dupT		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.1119-160dupT		intron_variant	Intron 1 of 1	1	NM_005360.5	ENSP00000327048.4
MAF	ENST00000393350.1	c.*4068dupT		3_prime_UTR_variant	Exon 1 of 1	6		ENSP00000377019.1
MAF	ENST00000569649.1	c.1118+4072dupT		intron_variant	Intron 1 of 1	5		ENSP00000455097.1

Frequencies

GnomAD3 genomes AF: 0.335 AC: 49049 AN: 146570 Hom.: 8416 Cov.: 0

Gnomad AFR AF: 0.237

Gnomad AMI AF: 0.300

Gnomad AMR AF: 0.350

Gnomad ASJ AF: 0.388

Gnomad EAS AF: 0.421

Gnomad SAS AF: 0.323

Gnomad FIN AF: 0.405

Gnomad MID AF: 0.385

Gnomad NFE AF: 0.372

Gnomad OTH AF: 0.339

GnomAD4 exome AF: 0.353 AC: 397544 AN: 1127032 Hom.: 40579 Cov.: 31 AF XY: 0.352 AC XY: 192818 AN XY: 547368

African (AFR) AF: 0.238 AC: 5716 AN: 23974

American (AMR) AF: 0.310 AC: 5090 AN: 16394

Ashkenazi Jewish (ASJ) AF: 0.371 AC: 6114 AN: 16500

East Asian (EAS) AF: 0.384 AC: 11132 AN: 28986

South Asian (SAS) AF: 0.319 AC: 16422 AN: 51516

European-Finnish (FIN) AF: 0.348 AC: 8238 AN: 23698

Middle Eastern (MID) AF: 0.388 AC: 1217 AN: 3140

European-Non Finnish (NFE) AF: 0.357 AC: 327556 AN: 916714

Other (OTH) AF: 0.348 AC: 16059 AN: 46110

GnomAD4 genome AF: 0.335 AC: 49062 AN: 146646 Hom.: 8418 Cov.: 0 AF XY: 0.339 AC XY: 24143 AN XY: 71230

African (AFR) AF: 0.237 AC: 9468 AN: 39894

American (AMR) AF: 0.349 AC: 5170 AN: 14800

Ashkenazi Jewish (ASJ) AF: 0.388 AC: 1337 AN: 3444

East Asian (EAS) AF: 0.421 AC: 2124 AN: 5050

South Asian (SAS) AF: 0.324 AC: 1510 AN: 4666

European-Finnish (FIN) AF: 0.405 AC: 3605 AN: 8892

Middle Eastern (MID) AF: 0.372 AC: 107 AN: 288

European-Non Finnish (NFE) AF: 0.372 AC: 24773 AN: 66672

Other (OTH) AF: 0.342 AC: 699 AN: 2042

Alfa AF: 0.00 Hom.: 0

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

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.44
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: rs36052284; hg19: chr16-79628609; COSMIC: COSV58154824;