Variant 16-79599908-TGCC-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1

The NM_005360.5(MAF):c.-9_-7delGGC variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.715 in 1,551,450 control chromosomes in the GnomAD database, including 384,130 homozygotes. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.77 ( 44286 hom., cov: 0)

Exomes 𝑓: 0.71 ( 339844 hom. )

Consequence

MAF
NM_005360.5 5_prime_UTR

Scores

Not classified

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: 0.735

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:

MAF (HGNC:):

MAF links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP6

Variant 16-79599908-TGCC-T is Benign according to our data. Variant chr16-79599908-TGCC-T is described in ClinVar as [Benign]. Clinvar id is 259752.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.903 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.-9_-7delGGC		5_prime_UTR_variant	1/2	ENST00000326043.5	NP_005351.2	O75444-1

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Protein	UniProt
MAF	ENST00000326043.5 linkuse as main transcript	c.-9_-7delGGC	5_prime_UTR_variant	1/2	1	NM_005360.5	ENSP00000327048.4	O75444-1
MAF	ENST00000393350.1 linkuse as main transcript	c.-9_-7delGGC	5_prime_UTR_variant	1/1	6		ENSP00000377019.1	O75444-2
MAF	ENST00000569649.1 linkuse as main transcript	c.-9_-7delGGC	upstream_gene_variant		5		ENSP00000455097.1	H3BP11

Frequencies

GnomAD3 genomes

AF:

0.765

AC:

115229

AN:

150592

Hom.:

44264

Cov.:

show subpopulations

Gnomad AFR

AF:

0.794

Gnomad AMI

AF:

0.723

Gnomad AMR

AF:

0.770

Gnomad ASJ

AF:

0.712

Gnomad EAS

AF:

0.926

Gnomad SAS

AF:

0.657

Gnomad FIN

AF:

0.820

Gnomad MID

AF:

0.769

Gnomad NFE

AF:

0.737

Gnomad OTH

AF:

0.765

GnomAD3 exomes

AF:

0.727

AC:

142149

AN:

195638

Hom.:

51816

AF XY:

0.720

AC XY:

79208

AN XY:

110086

show subpopulations

Gnomad AFR exome

AF:

0.754

Gnomad AMR exome

AF:

0.783

Gnomad ASJ exome

AF:

0.700

Gnomad EAS exome

AF:

0.906

Gnomad SAS exome

AF:

0.638

Gnomad FIN exome

AF:

0.776

Gnomad NFE exome

AF:

0.701

Gnomad OTH exome

AF:

0.717

GnomAD4 exome

AF:

0.709

AC:

993339

AN:

1400756

Hom.:

339844

AF XY:

0.706

AC XY:

492771

AN XY:

697712

show subpopulations

Gnomad4 AFR exome

AF:

0.752

Gnomad4 AMR exome

AF:

0.755

Gnomad4 ASJ exome

AF:

0.684

Gnomad4 EAS exome

AF:

0.878

Gnomad4 SAS exome

AF:

0.635

Gnomad4 FIN exome

AF:

0.744

Gnomad4 NFE exome

AF:

0.705

Gnomad4 OTH exome

AF:

0.711

GnomAD4 genome

AF:

0.765

AC:

115300

AN:

150694

Hom.:

44286

Cov.:

AF XY:

0.768

AC XY:

56543

AN XY:

73608

show subpopulations

Gnomad4 AFR

AF:

0.794

Gnomad4 AMR

AF:

0.770

Gnomad4 ASJ

AF:

0.712

Gnomad4 EAS

AF:

0.925

Gnomad4 SAS

AF:

0.656

Gnomad4 FIN

AF:

0.820

Gnomad4 NFE

AF:

0.737

Gnomad4 OTH

AF:

0.767

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

Ayme-Gripp syndrome

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Sep 05, 2021

- -

Cataract 21 multiple types

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Sep 05, 2021

- -

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Aug 15, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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