Variant 16-79594284-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_005360.5(MAF):c.*176A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.362 in 649,808 control chromosomes in the GnomAD database, including 43,906 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.34 ( 9012 hom., cov: 31)

Exomes 𝑓: 0.37 ( 34894 hom. )

Consequence

MAF
NM_005360.5 3_prime_UTR

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -2.01

Variant links:

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]

MAF links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BP6

Variant 16-79594284-T-C is Benign according to our data. Variant chr16-79594284-T-C is described in ClinVar as [Benign]. Clinvar id is 1263394.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.424 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MAF	NM_005360.5 linkuse as main transcript	c.*176A>G		3_prime_UTR_variant	2/2	ENST00000326043.5

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MAF	ENST00000326043.5 linkuse as main transcript	c.*176A>G	3_prime_UTR_variant	2/2	1	NM_005360.5	A2	O75444-1
MAF	ENST00000569649.1 linkuse as main transcript	c.1118+4501A>G	intron_variant		5		P4
MAF	ENST00000393350.1 linkuse as main transcript		downstream_gene_variant				A2	O75444-2

Frequencies

GnomAD3 genomes

AF:

0.338

AC:

51326

AN:

151898

Hom.:

9004

Cov.:

show subpopulations

Gnomad AFR

AF:

0.251

Gnomad AMI

AF:

0.295

Gnomad AMR

AF:

0.347

Gnomad ASJ

AF:

0.387

Gnomad EAS

AF:

0.440

Gnomad SAS

AF:

0.321

Gnomad FIN

AF:

0.398

Gnomad MID

AF:

0.383

Gnomad NFE

AF:

0.371

Gnomad OTH

AF:

0.340

GnomAD4 exome

AF:

0.369

AC:

183616

AN:

497794

Hom.:

34894

Cov.:

AF XY:

0.367

AC XY:

97202

AN XY:

264544

show subpopulations

Gnomad4 AFR exome

AF:

0.242

Gnomad4 AMR exome

AF:

0.308

Gnomad4 ASJ exome

AF:

0.399

Gnomad4 EAS exome

AF:

0.434

Gnomad4 SAS exome

AF:

0.329

Gnomad4 FIN exome

AF:

0.395

Gnomad4 NFE exome

AF:

0.376

Gnomad4 OTH exome

AF:

0.366

GnomAD4 genome

AF:

0.338

AC:

51354

AN:

152014

Hom.:

9012

Cov.:

AF XY:

0.342

AC XY:

25374

AN XY:

74278

show subpopulations

Gnomad4 AFR

AF:

0.251

Gnomad4 AMR

AF:

0.347

Gnomad4 ASJ

AF:

0.387

Gnomad4 EAS

AF:

0.439

Gnomad4 SAS

AF:

0.322

Gnomad4 FIN

AF:

0.398

Gnomad4 NFE

AF:

0.371

Gnomad4 OTH

AF:

0.344

Alfa

AF:

0.365

Hom.:

11451

Bravo

AF:

0.332

Asia WGS

AF:

0.334

AC:

1161

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 26, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

0.13

DANN

Benign

0.51

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over