16-79594639-AT-A

Variant names:

• chr16-79594639-AT-A
• rs66467731
• NM_005360.5:c.1119-87delA

Variant summary

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

The NM_005360.5(MAF):​c.1119-87delA variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.59 (26248 hom., cov: 0)
  • Exomes 𝑓: 0.58 (115560 hom.)
  • Failed GnomAD Quality Control
• Consequence: MAF NM_005360.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.184
• Publications: 7 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 16-79594639-AT-A is Benign according to our data. Variant chr16-79594639-AT-A is described in ClinVar as [Benign]. Clinvar id is 1245830.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.659 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MAF	NM_005360.5	c.1119-87delA		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.1119-87delA		intron_variant	Intron 1 of 1	1	NM_005360.5	ENSP00000327048.4
MAF	ENST00000393350.1	c.*4141delA		3_prime_UTR_variant	Exon 1 of 1	6		ENSP00000377019.1
MAF	ENST00000569649.1	c.1118+4145delA		intron_variant	Intron 1 of 1	5		ENSP00000455097.1

Frequencies

GnomAD3 genomes AF: 0.593 AC: 87147 AN: 146918 Hom.: 26242 Cov.: 0

Gnomad AFR AF: 0.460

Gnomad AMI AF: 0.660

Gnomad AMR AF: 0.595

Gnomad ASJ AF: 0.688

Gnomad EAS AF: 0.454

Gnomad SAS AF: 0.678

Gnomad FIN AF: 0.674

Gnomad MID AF: 0.663

Gnomad NFE AF: 0.661

Gnomad OTH AF: 0.590

GnomAD4 exome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.578 AC: 647943 AN: 1120232 Hom.: 115560 Cov.: 0 AF XY: 0.578 AC XY: 318589 AN XY: 551166

African (AFR) AF: 0.457 AC: 11360 AN: 24876

American (AMR) AF: 0.503 AC: 13326 AN: 26512

Ashkenazi Jewish (ASJ) AF: 0.579 AC: 11414 AN: 19710

East Asian (EAS) AF: 0.489 AC: 13755 AN: 28124

South Asian (SAS) AF: 0.570 AC: 34219 AN: 60010

European-Finnish (FIN) AF: 0.568 AC: 19753 AN: 34792

Middle Eastern (MID) AF: 0.592 AC: 2660 AN: 4490

European-Non Finnish (NFE) AF: 0.589 AC: 515474 AN: 875582

Other (OTH) AF: 0.563 AC: 25982 AN: 46136

GnomAD4 genome AF: 0.593 AC: 87167 AN: 146978 Hom.: 26248 Cov.: 0 AF XY: 0.596 AC XY: 42545 AN XY: 71358

African (AFR) AF: 0.460 AC: 18446 AN: 40130

American (AMR) AF: 0.595 AC: 8821 AN: 14824

Ashkenazi Jewish (ASJ) AF: 0.688 AC: 2369 AN: 3442

East Asian (EAS) AF: 0.453 AC: 2268 AN: 5010

South Asian (SAS) AF: 0.679 AC: 3148 AN: 4636

European-Finnish (FIN) AF: 0.674 AC: 5978 AN: 8876

Middle Eastern (MID) AF: 0.653 AC: 188 AN: 288

European-Non Finnish (NFE) AF: 0.661 AC: 44140 AN: 66822

Other (OTH) AF: 0.592 AC: 1208 AN: 2040

Alfa AF: 0.450 Hom.: 1119

Bravo AF: 0.580

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		0.18
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: rs66467731; hg19: chr16-79628536;