16-79598581-GGTGTGTGTGTGTGTGTGTGT-GGTGTGTGTGTGTGT

Variant names:

• chr16-79598581-GGTGTGT-G
• rs5818250
• NM_005360.5:c.1118+198_1118+203delACACAC

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2

The NM_001031804.3(MAF):​c.*194_*199delACACAC variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00357 in 1,409,968 control chromosomes in the GnomAD database, including 6 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.0024 (0 hom., cov: 0)
  • Exomes 𝑓: 0.0037 (6 hom.)
• Consequence: MAF NM_001031804.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.72

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]

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BS2: High AC in GnomAd4 at 336 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MAF	NM_005360.5	c.1118+198_1118+203delACACAC		intron_variant	Intron 1 of 1	ENST00000326043.5	NP_005351.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MAF	ENST00000326043.5	c.1118+198_1118+203delACACAC		intron_variant	Intron 1 of 1	1	NM_005360.5	ENSP00000327048.4
MAF	ENST00000393350.1	c.*194_*199delACACAC		3_prime_UTR_variant	Exon 1 of 1	6		ENSP00000377019.1
MAF	ENST00000569649.1	c.1118+198_1118+203delACACAC		intron_variant	Intron 1 of 1	5		ENSP00000455097.1

Frequencies

GnomAD3 genomes AF: 0.00241 AC: 331 AN: 137228 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.000749

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00268

Gnomad ASJ AF: 0.00270

Gnomad EAS AF: 0.00133

Gnomad SAS AF: 0.00405

Gnomad FIN AF: 0.000240

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00353

Gnomad OTH AF: 0.00381

GnomAD4 exome AF: 0.00370 AC: 4703 AN: 1272652 Hom.: 6 AF XY: 0.00374 AC XY: 2311 AN XY: 618394

Gnomad4 AFR exome AF: 0.00125

Gnomad4 AMR exome AF: 0.00224

Gnomad4 ASJ exome AF: 0.00414

Gnomad4 EAS exome AF: 0.000937

Gnomad4 SAS exome AF: 0.00360

Gnomad4 FIN exome AF: 0.000489

Gnomad4 NFE exome AF: 0.00399

Gnomad4 OTH exome AF: 0.00373

GnomAD4 genome AF: 0.00245 AC: 336 AN: 137316 Hom.: 0 Cov.: 0 AF XY: 0.00250 AC XY: 165 AN XY: 65918

Gnomad4 AFR AF: 0.000775

Gnomad4 AMR AF: 0.00268

Gnomad4 ASJ AF: 0.00270

Gnomad4 EAS AF: 0.00133

Gnomad4 SAS AF: 0.00406

Gnomad4 FIN AF: 0.000240

Gnomad4 NFE AF: 0.00355

Gnomad4 OTH AF: 0.00539

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5818250; hg19: chr16-79632478;