16-79594639-ATTTTT-ATTTTTT

Variant names:

• chr16-79594639-A-AT
• rs66467731
• NM_005360.5:c.1119-87dupA

Variant summary

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

The NM_001031804.3(MAF):​c.*4141dupA variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. 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: 0.0029 (0 hom.)
• Consequence: MAF NM_001031804.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.184

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 350 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MAF	NM_005360.5	c.1119-87dupA		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.1119-87dupA		intron_variant	Intron 1 of 1	1	NM_005360.5	ENSP00000327048.4
MAF	ENST00000393350	c.*4141dupA		3_prime_UTR_variant	Exon 1 of 1			ENSP00000377019.1
MAF	ENST00000569649.1	c.1118+4145dupA		intron_variant	Intron 1 of 1	5		ENSP00000455097.1

Frequencies

GnomAD3 genomes AF: 0.00233 AC: 343 AN: 147048 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.00562

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00149

Gnomad ASJ AF: 0.000290

Gnomad EAS AF: 0.0125

Gnomad SAS AF: 0.00193

Gnomad FIN AF: 0.000225

Gnomad MID AF: 0.00641

Gnomad NFE AF: 0.000150

Gnomad OTH AF: 0.00445

GnomAD4 exome AF: 0.00291 AC: 3345 AN: 1150180 Hom.: 0 Cov.: 0 AF XY: 0.00297 AC XY: 1679 AN XY: 566052

Gnomad4 AFR exome AF: 0.0112

Gnomad4 AMR exome AF: 0.00462

Gnomad4 ASJ exome AF: 0.00179

Gnomad4 EAS exome AF: 0.0157

Gnomad4 SAS exome AF: 0.00456

Gnomad4 FIN exome AF: 0.00301

Gnomad4 NFE exome AF: 0.00199

Gnomad4 OTH exome AF: 0.00484

GnomAD4 genome AF: 0.00238 AC: 350 AN: 147108 Hom.: 0 Cov.: 0 AF XY: 0.00244 AC XY: 174 AN XY: 71420

Gnomad4 AFR AF: 0.00575

Gnomad4 AMR AF: 0.00148

Gnomad4 ASJ AF: 0.000290

Gnomad4 EAS AF: 0.0125

Gnomad4 SAS AF: 0.00194

Gnomad4 FIN AF: 0.000225

Gnomad4 NFE AF: 0.000150

Gnomad4 OTH AF: 0.00441

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Other links and lift over

dbSNP: rs66467731; hg19: chr16-79628536;