16-79594639-AT-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_005360.5(MAF):c.1119-87del 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

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]

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
MAF	NM_005360.5	c.1119-87del		intron_variant		ENST00000326043.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MAF	ENST00000326043.5	c.1119-87del		intron_variant		1	NM_005360.5	A2
MAF	ENST00000393350.1	c.*4141del		3_prime_UTR_variant	1/1			A2
MAF	ENST00000569649.1	c.1118+4145del		intron_variant		5		P4

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

Gnomad4 AFR exome AF: 0.457

Gnomad4 AMR exome AF: 0.503

Gnomad4 ASJ exome AF: 0.579

Gnomad4 EAS exome AF: 0.489

Gnomad4 SAS exome AF: 0.570

Gnomad4 FIN exome AF: 0.568

Gnomad4 NFE exome AF: 0.589

Gnomad4 OTH exome AF: 0.563

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

Gnomad4 AFR AF: 0.460

Gnomad4 AMR AF: 0.595

Gnomad4 ASJ AF: 0.688

Gnomad4 EAS AF: 0.453

Gnomad4 SAS AF: 0.679

Gnomad4 FIN AF: 0.674

Gnomad4 NFE AF: 0.661

Gnomad4 OTH AF: 0.592

Bravo AF: 0.580

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Aug 15, 2019

- -

Computational scores

Source: dbNSFP v4.3

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

Publications

LitVar

Other links and lift over

dbSNP: rs66467731; hg19: chr16-79628536;