Variant 16-79599908-TGCCGCCGCCGCCGCC-TGCCGCC details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBS1BS2

The NM_005360.5(MAF):c.-15_-7delGGCGGCGGC variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00221 in 1,554,512 control chromosomes in the GnomAD database, including 52 homozygotes. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.011 ( 26 hom., cov: 0)

Exomes 𝑓: 0.0013 ( 26 hom. )

Consequence

MAF
NM_005360.5 5_prime_UTR

Scores

Not classified

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 3.29

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-TGCCGCCGCC-T is Benign according to our data. Variant chr16-79599908-TGCCGCCGCC-T is described in ClinVar as [Benign]. Clinvar id is 259751.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS1

Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0106 (1598/150802) while in subpopulation AFR AF= 0.0363 (1495/41170). AF 95% confidence interval is 0.0348. There are 26 homozygotes in gnomad4. There are 761 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.

BS2

High AC in GnomAd4 at 1598 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MAF	NM_005360.5 linkuse as main transcript	c.-15_-7delGGCGGCGGC		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.-15_-7delGGCGGCGGC	5_prime_UTR_variant	1/2	1	NM_005360.5	ENSP00000327048.4	O75444-1
MAF	ENST00000393350.1 linkuse as main transcript	c.-15_-7delGGCGGCGGC	5_prime_UTR_variant	1/1	6		ENSP00000377019.1	O75444-2
MAF	ENST00000569649.1 linkuse as main transcript	c.-15_-7delGGCGGCGGC	upstream_gene_variant		5		ENSP00000455097.1	H3BP11

Frequencies

GnomAD3 genomes

AF:

0.0106

AC:

1592

AN:

150700

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0363

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00362

Gnomad ASJ

AF:

0.00202

Gnomad EAS

AF:

0.000201

Gnomad SAS

AF:

0.000837

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000341

Gnomad OTH

AF:

0.00628

GnomAD3 exomes

AF:

0.00290

AC:

568

AN:

195638

Hom.:

AF XY:

0.00233

AC XY:

257

AN XY:

110086

show subpopulations

Gnomad AFR exome

AF:

0.0416

Gnomad AMR exome

AF:

0.00111

Gnomad ASJ exome

AF:

0.00251

Gnomad EAS exome

AF:

0.000356

Gnomad SAS exome

AF:

0.000253

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000506

Gnomad OTH exome

AF:

0.000808

GnomAD4 exome

AF:

0.00131

AC:

1839

AN:

1403710

Hom.:

AF XY:

0.00116

AC XY:

809

AN XY:

699332

show subpopulations

Gnomad4 AFR exome

AF:

0.0386

Gnomad4 AMR exome

AF:

0.00116

Gnomad4 ASJ exome

AF:

0.00284

Gnomad4 EAS exome

AF:

0.000213

Gnomad4 SAS exome

AF:

0.000225

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.000277

Gnomad4 OTH exome

AF:

0.00234

GnomAD4 genome

AF:

0.0106

AC:

1598

AN:

150802

Hom.:

Cov.:

AF XY:

0.0103

AC XY:

761

AN XY:

73660

show subpopulations

Gnomad4 AFR

AF:

0.0363

Gnomad4 AMR

AF:

0.00362

Gnomad4 ASJ

AF:

0.00202

Gnomad4 EAS

AF:

0.000201

Gnomad4 SAS

AF:

0.000838

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000341

Gnomad4 OTH

AF:

0.00621

ClinVar

Significance: Benign

Submissions summary: Benign:2

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

Jan 22, 2016

- -

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Aug 13, 2020

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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