16-79594639-ATT-A

Variant summary

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

The NM_005360.5(MAF):c.1119-88_1119-87del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0262 in 1,197,854 control chromosomes in the GnomAD database, including 139 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.019 (76 hom., cov: 0)
  • Exomes 𝑓: 0.027 (63 hom.)
• Consequence: MAF NM_005360.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.32

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-ATT-A is Benign according to our data. Variant chr16-79594639-ATT-A is described in ClinVar as [Benign]. Clinvar id is 1288364.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0626 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MAF	NM_005360.5	c.1119-88_1119-87del		intron_variant		ENST00000326043.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MAF	ENST00000326043.5	c.1119-88_1119-87del		intron_variant		1	NM_005360.5	A2
MAF	ENST00000393350.1	c.*4140_*4141del		3_prime_UTR_variant	1/1			A2
MAF	ENST00000569649.1	c.1118+4144_1118+4145del		intron_variant		5		P4

Frequencies

GnomAD3 genomes AF: 0.0194 AC: 2856 AN: 146946 Hom.: 76 Cov.: 0

Gnomad AFR AF: 0.0647

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00770

Gnomad ASJ AF: 0.000291

Gnomad EAS AF: 0.000397

Gnomad SAS AF: 0.000642

Gnomad FIN AF: 0.00316

Gnomad MID AF: 0.00962

Gnomad NFE AF: 0.00139

Gnomad OTH AF: 0.00988

GnomAD4 exome AF: 0.0271 AC: 28529 AN: 1050850 Hom.: 63 AF XY: 0.0281 AC XY: 14499 AN XY: 516164

Gnomad4 AFR exome AF: 0.0836

Gnomad4 AMR exome AF: 0.0320

Gnomad4 ASJ exome AF: 0.0412

Gnomad4 EAS exome AF: 0.0166

Gnomad4 SAS exome AF: 0.0385

Gnomad4 FIN exome AF: 0.0507

Gnomad4 NFE exome AF: 0.0233

Gnomad4 OTH exome AF: 0.0322

GnomAD4 genome AF: 0.0194 AC: 2858 AN: 147004 Hom.: 76 Cov.: 0 AF XY: 0.0193 AC XY: 1375 AN XY: 71358

Gnomad4 AFR AF: 0.0646

Gnomad4 AMR AF: 0.00762

Gnomad4 ASJ AF: 0.000291

Gnomad4 EAS AF: 0.000398

Gnomad4 SAS AF: 0.000430

Gnomad4 FIN AF: 0.00316

Gnomad4 NFE AF: 0.00139

Gnomad4 OTH AF: 0.00981

Alfa AF: 0.000240 Hom.: 1119

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 16, 2019

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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;