chr16-79598581-G-GGT

Position:

• chr16-79598581-G-GGT

Variant summary

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

The NM_005360.5(MAF):​c.1118+203_1118+204insAC variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.37 (9690 hom., cov: 0)
  • Exomes 𝑓: 0.33 (2600 hom.)
  • Failed GnomAD Quality Control
• Consequence: MAF NM_005360.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.149

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 16-79598581-G-GGT is Benign according to our data. Variant chr16-79598581-G-GGT is described in ClinVar as [Benign]. Clinvar id is 1234541.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.401 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MAF	NM_005360.5	c.1118+203_1118+204insAC		intron_variant		ENST00000326043.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MAF	ENST00000326043.5	c.1118+203_1118+204insAC		intron_variant		1	NM_005360.5	A2
MAF	ENST00000393350.1	c.*199_*200insAC		3_prime_UTR_variant	1/1			A2
MAF	ENST00000569649.1	c.1118+203_1118+204insAC		intron_variant		5		P4

Frequencies

GnomAD3 genomes AF: 0.375 AC: 51294 AN: 136850 Hom.: 9692 Cov.: 0

Gnomad AFR AF: 0.355

Gnomad AMI AF: 0.391

Gnomad AMR AF: 0.392

Gnomad ASJ AF: 0.306

Gnomad EAS AF: 0.0770

Gnomad SAS AF: 0.369

Gnomad FIN AF: 0.389

Gnomad MID AF: 0.366

Gnomad NFE AF: 0.405

Gnomad OTH AF: 0.378

GnomAD4 exome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.334 AC: 413573 AN: 1237440 Hom.: 2600 Cov.: 4 AF XY: 0.334 AC XY: 200916 AN XY: 601452

Gnomad4 AFR exome AF: 0.314

Gnomad4 AMR exome AF: 0.351

Gnomad4 ASJ exome AF: 0.275

Gnomad4 EAS exome AF: 0.132

Gnomad4 SAS exome AF: 0.317

Gnomad4 FIN exome AF: 0.354

Gnomad4 NFE exome AF: 0.343

Gnomad4 OTH exome AF: 0.326

GnomAD4 genome AF: 0.375 AC: 51297 AN: 136938 Hom.: 9690 Cov.: 0 AF XY: 0.371 AC XY: 24383 AN XY: 65718

Gnomad4 AFR AF: 0.355

Gnomad4 AMR AF: 0.391

Gnomad4 ASJ AF: 0.306

Gnomad4 EAS AF: 0.0774

Gnomad4 SAS AF: 0.367

Gnomad4 FIN AF: 0.389

Gnomad4 NFE AF: 0.405

Gnomad4 OTH AF: 0.374

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

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Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs5818250; hg19: chr16-79632478;