chr16-79598581-G-GGTGTGTGT

Position:

• chr16-79598581-G-GGTGTGTGT

Variant summary

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

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

• Frequency:
  • Genomes: 𝑓 0.011 (21 hom., cov: 0)
  • Exomes 𝑓: 0.012 (7 hom.)
  • Failed GnomAD Quality Control
• Consequence: MAF NM_005360.5 intron
• Clinical Significance: Likely 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 Likely_benign. Variant got -6 ACMG points.

• BP6: Variant 16-79598581-G-GGTGTGTGT is Benign according to our data. Variant chr16-79598581-G-GGTGTGTGT is described in ClinVar as [Likely_benign]. Clinvar id is 1344968.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS2: High AC in GnomAd4 at 1565 AD gene.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0114 AC: 1568 AN: 137208 Hom.: 21 Cov.: 0

Gnomad AFR AF: 0.00469

Gnomad AMI AF: 0.0138

Gnomad AMR AF: 0.0107

Gnomad ASJ AF: 0.0501

Gnomad EAS AF: 0.00398

Gnomad SAS AF: 0.00557

Gnomad FIN AF: 0.00876

Gnomad MID AF: 0.0207

Gnomad NFE AF: 0.0144

Gnomad OTH AF: 0.0142

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0121 AC: 15379 AN: 1269764 Hom.: 7 Cov.: 4 AF XY: 0.0118 AC XY: 7263 AN XY: 617096

Gnomad4 AFR exome AF: 0.00339

Gnomad4 AMR exome AF: 0.00894

Gnomad4 ASJ exome AF: 0.0531

Gnomad4 EAS exome AF: 0.00341

Gnomad4 SAS exome AF: 0.00650

Gnomad4 FIN exome AF: 0.0106

Gnomad4 NFE exome AF: 0.0123

Gnomad4 OTH exome AF: 0.0135

GnomAD4 genome AF: 0.0114 AC: 1565 AN: 137296 Hom.: 21 Cov.: 0 AF XY: 0.0111 AC XY: 732 AN XY: 65910

Gnomad4 AFR AF: 0.00468

Gnomad4 AMR AF: 0.0107

Gnomad4 ASJ AF: 0.0501

Gnomad4 EAS AF: 0.00376

Gnomad4 SAS AF: 0.00532

Gnomad4 FIN AF: 0.00876

Gnomad4 NFE AF: 0.0144

Gnomad4 OTH AF: 0.0140

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

GeneDx

Aug 14, 2020

- -

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;