Genetic Variant NM_005360.5:c.1118+196_1118+203delACACACAC (chr16-79598581-GGTGTGTGT-G) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_005360.5(MAF):c.1118+196_1118+203delACACACAC variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000161 in 1,410,636 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.00015 ( 0 hom., cov: 0)

Exomes 𝑓: 0.00016 ( 0 hom. )

Consequence

MAF
NM_005360.5 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.92

Publications

4 publications found

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 Gene-Disease associations (from GenCC):

Ayme-Gripp syndrome
Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics, G2P
cataract 21 multiple types
Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: G2P, Ambry Genetics
cataract - microcornea syndrome
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
cerulean cataract
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
pulverulent cataract
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
Fine-Lubinsky syndrome
Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

MAF links:

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MAF	NM_005360.5 link	c.1118+196_1118+203delACACACAC		intron_variant	Intron 1 of 1	ENST00000326043.5	NP_005351.2	O75444-1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
MAF	ENST00000326043.5 link	c.1118+196_1118+203delACACACAC	intron_variant	Intron 1 of 1	1	NM_005360.5	ENSP00000327048.4	O75444-1
MAF	ENST00000393350.1 link	c.192_199delACACACAC	3_prime_UTR_variant	Exon 1 of 1	6		ENSP00000377019.1	O75444-2
MAF	ENST00000569649.1 link	c.1118+196_1118+203delACACACAC	intron_variant	Intron 1 of 1	5		ENSP00000455097.1	H3BP11

Frequencies

GnomAD3 genomes

AF:

0.000146

AC:

AN:

137232

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000832

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0000725

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.000221

Gnomad SAS

AF:

0.000759

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000171

Gnomad OTH

AF:

0.000545

GnomAD4 exome

AF:

0.000163

AC:

207

AN:

1273316

Hom.:

AF XY:

0.000179

AC XY:

111

AN XY:

618746

show subpopulations

African (AFR)

AF:

0.000102

AC:

AN:

29534

American (AMR)

AF:

0.000136

AC:

AN:

29436

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

20060

East Asian (EAS)

AF:

0.000151

AC:

AN:

33182

South Asian (SAS)

AF:

0.000540

AC:

AN:

66698

European-Finnish (FIN)

AF:

0.0000349

AC:

AN:

28622

Middle Eastern (MID)

AF:

0.000555

AC:

AN:

3606

European-Non Finnish (NFE)

AF:

0.000140

AC:

141

AN:

1009268

Other (OTH)

AF:

0.000284

AC:

AN:

52910

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.477

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.000146

AC:

AN:

137320

Hom.:

Cov.:

AF XY:

0.000182

AC XY:

AN XY:

65920

show subpopulations

African (AFR)

AF:

0.0000830

AC:

AN:

36148

American (AMR)

AF:

0.0000725

AC:

AN:

13800

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3336

East Asian (EAS)

AF:

0.000221

AC:

AN:

4518

South Asian (SAS)

AF:

0.000761

AC:

AN:

3944

European-Finnish (FIN)

AF:

0.00

AC:

AN:

8344

Middle Eastern (MID)

AF:

0.00

AC:

AN:

270

European-Non Finnish (NFE)

AF:

0.000171

AC:

AN:

64238

Other (OTH)

AF:

0.000539

AC:

AN:

1854

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.542

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.00

Hom.:

370

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

1.9

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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NM_005360.5:c.1118+196_1118+203delACACACAC

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over