dbSNP rs2288066: MAF:c.-780T>G (chr16-79600682-A-C) – ACMG Classification: Benign (-20 pts)

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

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

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.203

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:

LOC101928230 (HGNC:):

LOC101928230 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 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_multiple_submitters_no_conflicts, 2 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 rank	MANE	Protein	UniProt
MAF	NM_005360.5 link	c.-780T>G		5_prime_UTR_variant	Exon 1 of 2	ENST00000326043.5	NP_005351.2	O75444-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MAF	ENST00000326043.5 link	c.-780T>G		5_prime_UTR_variant	Exon 1 of 2	1	NM_005360.5	ENSP00000327048.4		O75444-1
MAF	ENST00000393350.1 link	c.-780T>G		5_prime_UTR_variant	Exon 1 of 1	6		ENSP00000377019.1		O75444-2

Frequencies

GnomAD3 genomes

AF:

0.109

AC:

16547

AN:

151534

Hom.:

1305

Cov.:

show subpopulations

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.:

AF XY:

0.148

AC XY:

3037

AN XY:

20544

show subpopulations

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.:

AF XY:

0.111

AC XY:

8230

AN XY:

74068

show subpopulations

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:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Jul 07, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.73

CADD

Benign

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

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