16-79599908-TGCCGCCGCCGCCGCC-TGCCGCCGCC

Position:

• chr16-79599908-TGCCGCCGCCGCCGCC-TGCCGCCGCC

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_Moderate BS2

The NM_005360.5(MAF):​c.-12_-7del variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000335 in 1,466,666 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.00017 (0 hom., cov: 0)
  • Exomes 𝑓: 0.00035 (0 hom.)
• Consequence: MAF NM_005360.5 5_prime_UTR
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.63

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 Likely_benign. Variant got -6 ACMG points.

• BP6: Variant 16-79599908-TGCCGCC-T is Benign according to our data. Variant chr16-79599908-TGCCGCC-T is described in ClinVar as [Likely_benign]. Clinvar id is 2646891.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS2: High AC in GnomAd4 at 26 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MAF	NM_005360.5	c.-12_-7del		5_prime_UTR_variant	1/2	ENST00000326043.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MAF	ENST00000326043.5	c.-12_-7del		5_prime_UTR_variant	1/2	1	NM_005360.5	A2
MAF	ENST00000393350.1	c.-12_-7del		5_prime_UTR_variant	1/1			A2
MAF	ENST00000569649.1			upstream_gene_variant		5		P4

Frequencies

GnomAD3 genomes AF: 0.000173 AC: 26 AN: 150622 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.0000244

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000857

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000209

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000163

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.00135 AC: 265 AN: 195638 Hom.: 1 AF XY: 0.00128 AC XY: 141 AN XY: 110086

Gnomad AFR exome AF: 0.00230

Gnomad AMR exome AF: 0.00289

Gnomad ASJ exome AF: 0.000455

Gnomad EAS exome AF: 0.00142

Gnomad SAS exome AF: 0.00101

Gnomad FIN exome AF: 0.00158

Gnomad NFE exome AF: 0.000889

Gnomad OTH exome AF: 0.00121

GnomAD4 exome AF: 0.000354 AC: 466 AN: 1315942 Hom.: 0 AF XY: 0.000369 AC XY: 242 AN XY: 656058

Gnomad4 AFR exome AF: 0.000268

Gnomad4 AMR exome AF: 0.00222

Gnomad4 ASJ exome AF: 0.000210

Gnomad4 EAS exome AF: 0.000639

Gnomad4 SAS exome AF: 0.000450

Gnomad4 FIN exome AF: 0.000889

Gnomad4 NFE exome AF: 0.000258

Gnomad4 OTH exome AF: 0.000239

GnomAD4 genome AF: 0.000173 AC: 26 AN: 150724 Hom.: 0 Cov.: 0 AF XY: 0.000163 AC XY: 12 AN XY: 73622

Gnomad4 AFR AF: 0.0000243

Gnomad4 AMR AF: 0.000856

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000209

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000163

Gnomad4 OTH AF: 0.00

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Jul 01, 2024

MAF: BS1 -

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: rs5818251; hg19: chr16-79633805;