16-79598581-G-GGTGT

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+204insACAC variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.23 (3660 hom., cov: 0)
  • Exomes 𝑓: 0.20 (874 hom.)
• 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-GGTGT is Benign according to our data. Variant chr16-79598581-G-GGTGT is described in ClinVar as [Benign]. Clinvar id is 1274209.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.361 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.234 AC: 32014 AN: 136938 Hom.: 3651 Cov.: 0

Gnomad AFR AF: 0.238

Gnomad AMI AF: 0.156

Gnomad AMR AF: 0.247

Gnomad ASJ AF: 0.285

Gnomad EAS AF: 0.375

Gnomad SAS AF: 0.232

Gnomad FIN AF: 0.235

Gnomad MID AF: 0.299

Gnomad NFE AF: 0.217

Gnomad OTH AF: 0.223

GnomAD4 exome AF: 0.199 AC: 250212 AN: 1258996 Hom.: 874 Cov.: 4 AF XY: 0.199 AC XY: 121462 AN XY: 611852

Gnomad4 AFR exome AF: 0.209

Gnomad4 AMR exome AF: 0.240

Gnomad4 ASJ exome AF: 0.239

Gnomad4 EAS exome AF: 0.320

Gnomad4 SAS exome AF: 0.204

Gnomad4 FIN exome AF: 0.189

Gnomad4 NFE exome AF: 0.192

Gnomad4 OTH exome AF: 0.202

GnomAD4 genome AF: 0.234 AC: 32048 AN: 137026 Hom.: 3660 Cov.: 0 AF XY: 0.237 AC XY: 15564 AN XY: 65770

Gnomad4 AFR AF: 0.238

Gnomad4 AMR AF: 0.247

Gnomad4 ASJ AF: 0.285

Gnomad4 EAS AF: 0.376

Gnomad4 SAS AF: 0.233

Gnomad4 FIN AF: 0.235

Gnomad4 NFE AF: 0.217

Gnomad4 OTH AF: 0.225

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;