Variant 16-79594427-GA-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_005360.5(MAF):c.*32del variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0807 in 1,529,704 control chromosomes in the GnomAD database, including 5,585 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.063 ( 428 hom., cov: 31)

Exomes 𝑓: 0.083 ( 5157 hom. )

Consequence

MAF
NM_005360.5 3_prime_UTR

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.852

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 -10 ACMG points.

BP6

Variant 16-79594427-GA-G is Benign according to our data. Variant chr16-79594427-GA-G is described in ClinVar as [Benign]. Clinvar id is 1236763.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0967 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MAF	NM_005360.5 linkuse as main transcript	c.*32del		3_prime_UTR_variant	2/2	ENST00000326043.5	NP_005351.2

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MAF	ENST00000326043.5 linkuse as main transcript	c.*32del	3_prime_UTR_variant	2/2	1	NM_005360.5	ENSP00000327048	A2	O75444-1
MAF	ENST00000393350.1 linkuse as main transcript	c.*4353del	3_prime_UTR_variant	1/1			ENSP00000377019	A2	O75444-2
MAF	ENST00000569649.1 linkuse as main transcript	c.1118+4357del	intron_variant		5		ENSP00000455097	P4

Frequencies

GnomAD3 genomes

AF:

0.0634

AC:

9637

AN:

151942

Hom.:

428

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0144

Gnomad AMI

AF:

0.0757

Gnomad AMR

AF:

0.0459

Gnomad ASJ

AF:

0.144

Gnomad EAS

AF:

0.00212

Gnomad SAS

AF:

0.104

Gnomad FIN

AF:

0.0964

Gnomad MID

AF:

0.133

Gnomad NFE

AF:

0.0891

Gnomad OTH

AF:

0.0690

GnomAD3 exomes

AF:

0.0793

AC:

12470

AN:

157210

Hom.:

662

AF XY:

0.0843

AC XY:

6975

AN XY:

82740

show subpopulations

Gnomad AFR exome

AF:

0.0135

Gnomad AMR exome

AF:

0.0370

Gnomad ASJ exome

AF:

0.156

Gnomad EAS exome

AF:

0.00185

Gnomad SAS exome

AF:

0.110

Gnomad FIN exome

AF:

0.0990

Gnomad NFE exome

AF:

0.0925

Gnomad OTH exome

AF:

0.0904

GnomAD4 exome

AF:

0.0826

AC:

113856

AN:

1377644

Hom.:

5157

Cov.:

AF XY:

0.0836

AC XY:

56886

AN XY:

680774

show subpopulations

Gnomad4 AFR exome

AF:

0.0118

Gnomad4 AMR exome

AF:

0.0392

Gnomad4 ASJ exome

AF:

0.153

Gnomad4 EAS exome

AF:

0.00107

Gnomad4 SAS exome

AF:

0.109

Gnomad4 FIN exome

AF:

0.0968

Gnomad4 NFE exome

AF:

0.0844

Gnomad4 OTH exome

AF:

0.0832

GnomAD4 genome

AF:

0.0633

AC:

9630

AN:

152060

Hom.:

428

Cov.:

AF XY:

0.0630

AC XY:

4684

AN XY:

74296

show subpopulations

Gnomad4 AFR

AF:

0.0144

Gnomad4 AMR

AF:

0.0457

Gnomad4 ASJ

AF:

0.144

Gnomad4 EAS

AF:

0.00213

Gnomad4 SAS

AF:

0.104

Gnomad4 FIN

AF:

0.0964

Gnomad4 NFE

AF:

0.0891

Gnomad4 OTH

AF:

0.0687

Alfa

AF:

0.0603

Hom.:

107

Bravo

AF:

0.0555

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

Aug 07, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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