16-79598581-GGT-G

Position:

• chr16-79598581-GGT-G

Variant summary

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

The NM_005360.5(MAF):​c.1118+202_1118+203del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.129 in 1,382,978 control chromosomes in the GnomAD database, including 2,291 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.13 (1256 hom., cov: 0)
  • Exomes 𝑓: 0.13 (1035 hom.)
• Consequence: MAF NM_005360.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.778

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-GGT-G is Benign according to our data. Variant chr16-79598581-GGT-G is described in ClinVar as [Benign]. Clinvar id is 1180410.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.352 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MAF	NM_005360.5	c.1118+202_1118+203del		intron_variant		ENST00000326043.5	NP_005351.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MAF	ENST00000326043.5	c.1118+202_1118+203del		intron_variant		1	NM_005360.5	ENSP00000327048	A2
MAF	ENST00000393350.1	c.*198_*199del		3_prime_UTR_variant	1/1			ENSP00000377019	A2
MAF	ENST00000569649.1	c.1118+202_1118+203del		intron_variant		5		ENSP00000455097	P4

Frequencies

GnomAD3 genomes AF: 0.128 AC: 17581 AN: 137042 Hom.: 1255 Cov.: 0

Gnomad AFR AF: 0.101

Gnomad AMI AF: 0.129

Gnomad AMR AF: 0.127

Gnomad ASJ AF: 0.177

Gnomad EAS AF: 0.366

Gnomad SAS AF: 0.133

Gnomad FIN AF: 0.0885

Gnomad MID AF: 0.100

Gnomad NFE AF: 0.130

Gnomad OTH AF: 0.131

GnomAD4 exome AF: 0.129 AC: 160262 AN: 1245848 Hom.: 1035 AF XY: 0.129 AC XY: 78098 AN XY: 605650

Gnomad4 AFR exome AF: 0.108

Gnomad4 AMR exome AF: 0.0984

Gnomad4 ASJ exome AF: 0.171

Gnomad4 EAS exome AF: 0.290

Gnomad4 SAS exome AF: 0.127

Gnomad4 FIN exome AF: 0.0993

Gnomad4 NFE exome AF: 0.125

Gnomad4 OTH exome AF: 0.134

GnomAD4 genome AF: 0.128 AC: 17586 AN: 137130 Hom.: 1256 Cov.: 0 AF XY: 0.128 AC XY: 8422 AN XY: 65816

Gnomad4 AFR AF: 0.101

Gnomad4 AMR AF: 0.127

Gnomad4 ASJ AF: 0.177

Gnomad4 EAS AF: 0.367

Gnomad4 SAS AF: 0.133

Gnomad4 FIN AF: 0.0885

Gnomad4 NFE AF: 0.130

Gnomad4 OTH AF: 0.130

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 18, 2019

- -

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: rs5818250; hg19: chr16-79632478;