NM_005360.5:c.1118+200_1118+203dupACAC

Variant names:

• chr16-79598581-G-GGTGT
• rs5818250
• NM_005360.5:c.1118+200_1118+203dupACAC

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_005360.5(MAF):​c.1118+200_1118+203dupACAC variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.23 (3660 hom., cov: 0)
  • Exomes 𝑓: 0.20 (874 hom.)
• Consequence: MAF NM_005360.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.149
• Publications: 4 publications found

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), G2P, Ambry Genetics
• 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

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP6: Variant 16-79598581-G-GGTGT is Benign according to our data. Variant chr16-79598581-G-GGTGT is described in ClinVar as Benign. ClinVar VariationId is 1274209.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.361 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005360.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAF	NM_005360.5	MANE Select	c.1118+200_1118+203dupACAC		intron	N/A	NP_005351.2
	MAF	NM_001031804.3		c.*196_*199dupACAC		3_prime_UTR	Exon 1 of 1	NP_001026974.1	O75444-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAF	ENST00000326043.5	TSL:1 MANE Select	c.1118+200_1118+203dupACAC		intron	N/A	ENSP00000327048.4	O75444-1
	MAF	ENST00000393350.1	TSL:6	c.*196_*199dupACAC		3_prime_UTR	Exon 1 of 1	ENSP00000377019.1	O75444-2
	MAF	ENST00000569649.1	TSL:5	c.1118+200_1118+203dupACAC		intron	N/A	ENSP00000455097.1	H3BP11

Frequencies

GnomAD3 genomes AF: 0.234 AC: 32014 AN: 136938 Hom.: 3651 Cov.: 0

Gnomad AFR AF: 0.238

Gnomad AMI AF: 0.156

Gnomad AMR AF: 0.247

Gnomad ASJ AF: 0.285

Gnomad EAS AF: 0.375

Gnomad SAS AF: 0.232

Gnomad FIN AF: 0.235

Gnomad MID AF: 0.299

Gnomad NFE AF: 0.217

Gnomad OTH AF: 0.223

GnomAD4 exome AF: 0.199 AC: 250212 AN: 1258996 Hom.: 874 Cov.: 4 AF XY: 0.199 AC XY: 121462 AN XY: 611852

African (AFR) AF: 0.209 AC: 6110 AN: 29168

American (AMR) AF: 0.240 AC: 6978 AN: 29078

Ashkenazi Jewish (ASJ) AF: 0.239 AC: 4734 AN: 19838

East Asian (EAS) AF: 0.320 AC: 10457 AN: 32672

South Asian (SAS) AF: 0.204 AC: 13438 AN: 65816

European-Finnish (FIN) AF: 0.189 AC: 5369 AN: 28380

Middle Eastern (MID) AF: 0.201 AC: 714 AN: 3560

European-Non Finnish (NFE) AF: 0.192 AC: 191837 AN: 998088

Other (OTH) AF: 0.202 AC: 10575 AN: 52396

GnomAD4 genome AF: 0.234 AC: 32048 AN: 137026 Hom.: 3660 Cov.: 0 AF XY: 0.237 AC XY: 15564 AN XY: 65770

African (AFR) AF: 0.238 AC: 8599 AN: 36074

American (AMR) AF: 0.247 AC: 3404 AN: 13766

Ashkenazi Jewish (ASJ) AF: 0.285 AC: 948 AN: 3326

East Asian (EAS) AF: 0.376 AC: 1692 AN: 4504

South Asian (SAS) AF: 0.233 AC: 917 AN: 3942

European-Finnish (FIN) AF: 0.235 AC: 1948 AN: 8306

Middle Eastern (MID) AF: 0.287 AC: 77 AN: 268

European-Non Finnish (NFE) AF: 0.217 AC: 13912 AN: 64128

Other (OTH) AF: 0.225 AC: 416 AN: 1846

Alfa AF: 0.191 Hom.: 370

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.15
Mutation Taster		=99/1	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs5818250; hg19: chr16-79632478; COSMIC: COSV58153344; COSMIC: COSV58153344;