chr16-79598581-G-GGTGTGT

Position:

• chr16-79598581-G-GGTGTGT

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+204insACACAC 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 0.033 (120 hom., cov: 0)
  • Exomes 𝑓: 0.025 (32 hom.)
• 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 Benign. Variant got -10 ACMG points.

• BP6: Variant 16-79598581-G-GGTGTGT is Benign according to our data. Variant chr16-79598581-G-GGTGTGT is described in ClinVar as [Likely_benign]. Clinvar id is 1207043.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.125 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0327 AC: 4484 AN: 137176 Hom.: 119 Cov.: 0

Gnomad AFR AF: 0.0307

Gnomad AMI AF: 0.0495

Gnomad AMR AF: 0.0750

Gnomad ASJ AF: 0.0222

Gnomad EAS AF: 0.134

Gnomad SAS AF: 0.0818

Gnomad FIN AF: 0.0216

Gnomad MID AF: 0.0138

Gnomad NFE AF: 0.0164

Gnomad OTH AF: 0.0327

GnomAD4 exome AF: 0.0254 AC: 32190 AN: 1268486 Hom.: 32 Cov.: 4 AF XY: 0.0270 AC XY: 16654 AN XY: 616330

Gnomad4 AFR exome AF: 0.0272

Gnomad4 AMR exome AF: 0.0860

Gnomad4 ASJ exome AF: 0.0236

Gnomad4 EAS exome AF: 0.124

Gnomad4 SAS exome AF: 0.0828

Gnomad4 FIN exome AF: 0.0205

Gnomad4 NFE exome AF: 0.0164

Gnomad4 OTH exome AF: 0.0308

GnomAD4 genome AF: 0.0327 AC: 4495 AN: 137264 Hom.: 120 Cov.: 0 AF XY: 0.0362 AC XY: 2385 AN XY: 65892

Gnomad4 AFR AF: 0.0308

Gnomad4 AMR AF: 0.0753

Gnomad4 ASJ AF: 0.0222

Gnomad4 EAS AF: 0.134

Gnomad4 SAS AF: 0.0830

Gnomad4 FIN AF: 0.0216

Gnomad4 NFE AF: 0.0164

Gnomad4 OTH AF: 0.0324

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

Feb 06, 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;