rs2288066

chr16-79600682-A-Cchr16-79600682-A-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_005360.5(MAF):c.-780T>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.117 in 195,718 control chromosomes in the GnomAD database, including 1,977 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.11 (1309 hom., cov: 29)
  • Exomes 𝑓: 0.14 (668 hom.)
• Consequence: MAF NM_005360.5 5_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.203

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 -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BP6: Variant 16-79600682-A-C is Benign according to our data. Variant chr16-79600682-A-C is described in ClinVar as [Benign]. Clinvar id is 1251859.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.349 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MAF	NM_005360.5	c.-780T>G		5_prime_UTR_variant	1/2	ENST00000326043.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MAF	ENST00000326043.5	c.-780T>G		5_prime_UTR_variant	1/2	1	NM_005360.5	A2
MAF	ENST00000393350.1	c.-780T>G		5_prime_UTR_variant	1/1			A2

Frequencies

GnomAD3 genomes AF: 0.109 AC: 16547 AN: 151534 Hom.: 1305 Cov.: 29

Gnomad AFR AF: 0.0280

Gnomad AMI AF: 0.139

Gnomad AMR AF: 0.178

Gnomad ASJ AF: 0.157

Gnomad EAS AF: 0.364

Gnomad SAS AF: 0.163

Gnomad FIN AF: 0.0831

Gnomad MID AF: 0.122

Gnomad NFE AF: 0.122

Gnomad OTH AF: 0.105

GnomAD4 exome AF: 0.145 AC: 6384 AN: 44066 Hom.: 668 Cov.: 0 AF XY: 0.148 AC XY: 3037 AN XY: 20544

Gnomad4 AFR exome AF: 0.0251

Gnomad4 AMR exome AF: 0.171

Gnomad4 ASJ exome AF: 0.162

Gnomad4 EAS exome AF: 0.378

Gnomad4 SAS exome AF: 0.145

Gnomad4 FIN exome AF: 0.0869

Gnomad4 NFE exome AF: 0.119

Gnomad4 OTH exome AF: 0.136

GnomAD4 genome AF: 0.109 AC: 16554 AN: 151652 Hom.: 1309 Cov.: 29 AF XY: 0.111 AC XY: 8230 AN XY: 74068

Gnomad4 AFR AF: 0.0279

Gnomad4 AMR AF: 0.179

Gnomad4 ASJ AF: 0.157

Gnomad4 EAS AF: 0.363

Gnomad4 SAS AF: 0.164

Gnomad4 FIN AF: 0.0831

Gnomad4 NFE AF: 0.122

Gnomad4 OTH AF: 0.109

Alfa AF: 0.109 Hom.: 324

Bravo AF: 0.114

Asia WGS AF: 0.217 AC: 755 AN: 3478

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

Jul 07, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
Cadd	Benign	15
Dann	Benign	0.82

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: rs2288066; hg19: chr16-79634579;