Variant chr16-79598581-GGTGT-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2

The NM_005360.5(MAF):c.1118+200_1118+203del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00526 in 1,396,890 control chromosomes in the GnomAD database, including 34 homozygotes. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.012 ( 30 hom., cov: 0)

Exomes 𝑓: 0.0045 ( 4 hom. )

Consequence

MAF
NM_005360.5 intron

Scores

Not classified

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.66

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 16-79598581-GGTGT-G is Benign according to our data. Variant chr16-79598581-GGTGT-G is described in ClinVar as [Likely_benign]. Clinvar id is 1196267.Status of the report is criteria_provided_single_submitter, 1 stars.

BS1

Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0121 (1662/137288) while in subpopulation AFR AF= 0.0412 (1488/36136). AF 95% confidence interval is 0.0394. There are 30 homozygotes in gnomad4. There are 780 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.

BS2

High AC in GnomAd4 at 1662 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MAF	NM_005360.5 linkuse as main transcript	c.1118+200_1118+203del		intron_variant		ENST00000326043.5

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MAF	ENST00000326043.5 linkuse as main transcript	c.1118+200_1118+203del	intron_variant		1	NM_005360.5	A2	O75444-1
MAF	ENST00000393350.1 linkuse as main transcript	c.196_199del	3_prime_UTR_variant	1/1			A2	O75444-2
MAF	ENST00000569649.1 linkuse as main transcript	c.1118+200_1118+203del	intron_variant		5		P4

Frequencies

GnomAD3 genomes

AF:

0.0120

AC:

1644

AN:

137200

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0408

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00522

Gnomad ASJ

AF:

0.00150

Gnomad EAS

AF:

0.000663

Gnomad SAS

AF:

0.000506

Gnomad FIN

AF:

0.000120

Gnomad MID

AF:

0.0103

Gnomad NFE

AF:

0.000918

Gnomad OTH

AF:

0.0147

GnomAD4 exome

AF:

0.00452

AC:

5689

AN:

1259602

Hom.:

AF XY:

0.00451

AC XY:

2762

AN XY:

612094

show subpopulations

Gnomad4 AFR exome

AF:

0.0437

Gnomad4 AMR exome

AF:

0.00594

Gnomad4 ASJ exome

AF:

0.00776

Gnomad4 EAS exome

AF:

0.0204

Gnomad4 SAS exome

AF:

0.00334

Gnomad4 FIN exome

AF:

0.00302

Gnomad4 NFE exome

AF:

0.00273

Gnomad4 OTH exome

AF:

0.00720

GnomAD4 genome

AF:

0.0121

AC:

1662

AN:

137288

Hom.:

Cov.:

AF XY:

0.0118

AC XY:

780

AN XY:

65900

show subpopulations

Gnomad4 AFR

AF:

0.0412

Gnomad4 AMR

AF:

0.00522

Gnomad4 ASJ

AF:

0.00150

Gnomad4 EAS

AF:

0.000665

Gnomad4 SAS

AF:

0.000507

Gnomad4 FIN

AF:

0.000120

Gnomad4 NFE

AF:

0.000919

Gnomad4 OTH

AF:

0.0146

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

GeneDx

Aug 31, 2019

- -

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