chr16-79599908-TGCCGCCGCCGCC-T

Position:

• chr16-79599908-TGCCGCCGCCGCC-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP6_Very_Strong BS2

The NM_005360.5(MAF):​c.-18_-7delGGCGGCGGCGGC variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00319 in 1,554,540 control chromosomes in the GnomAD database, including 16 homozygotes. Variant has been reported in ClinVar as Likely benign (★★).

• Frequency:
  • Genomes: 𝑓 0.0024 (3 hom., cov: 0)
  • Exomes 𝑓: 0.0033 (13 hom.)
• Consequence: MAF NM_005360.5 5_prime_UTR
• Clinical Significance: Likely benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 3.29

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP6: Variant 16-79599908-TGCCGCCGCCGCC-T is Benign according to our data. Variant chr16-79599908-TGCCGCCGCCGCC-T is described in ClinVar as [Likely_benign]. Clinvar id is 803278.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BS2: High AC in GnomAd4 at 368 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MAF	NM_005360.5	c.-18_-7delGGCGGCGGCGGC		5_prime_UTR_variant	1/2	ENST00000326043.5	NP_005351.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MAF	ENST00000326043.5	c.-18_-7delGGCGGCGGCGGC		5_prime_UTR_variant	1/2	1	NM_005360.5	ENSP00000327048.4
MAF	ENST00000393350.1	c.-18_-7delGGCGGCGGCGGC		5_prime_UTR_variant	1/1	6		ENSP00000377019.1
MAF	ENST00000569649.1	c.-18_-7delGGCGGCGGCGGC		upstream_gene_variant		5		ENSP00000455097.1

Frequencies

GnomAD3 genomes AF: 0.00244 AC: 368 AN: 150702 Hom.: 3 Cov.: 0

Gnomad AFR AF: 0.000609

Gnomad AMI AF: 0.00222

Gnomad AMR AF: 0.00395

Gnomad ASJ AF: 0.00434

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00732

Gnomad FIN AF: 0.000288

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00335

Gnomad OTH AF: 0.000966

GnomAD3 exomes AF: 0.00299 AC: 584 AN: 195638 Hom.: 0 AF XY: 0.00347 AC XY: 382 AN XY: 110086

Gnomad AFR exome AF: 0.000368

Gnomad AMR exome AF: 0.00229

Gnomad ASJ exome AF: 0.00342

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00572

Gnomad FIN exome AF: 0.000559

Gnomad NFE exome AF: 0.00340

Gnomad OTH exome AF: 0.00323

GnomAD4 exome AF: 0.00327 AC: 4595 AN: 1403736 Hom.: 13 AF XY: 0.00345 AC XY: 2416 AN XY: 699342

Gnomad4 AFR exome AF: 0.000588

Gnomad4 AMR exome AF: 0.00213

Gnomad4 ASJ exome AF: 0.00323

Gnomad4 EAS exome AF: 0.0000267

Gnomad4 SAS exome AF: 0.00571

Gnomad4 FIN exome AF: 0.000706

Gnomad4 NFE exome AF: 0.00339

Gnomad4 OTH exome AF: 0.00361

GnomAD4 genome AF: 0.00244 AC: 368 AN: 150804 Hom.: 3 Cov.: 0 AF XY: 0.00231 AC XY: 170 AN XY: 73662

Gnomad4 AFR AF: 0.000607

Gnomad4 AMR AF: 0.00395

Gnomad4 ASJ AF: 0.00434

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00733

Gnomad4 FIN AF: 0.000288

Gnomad4 NFE AF: 0.00335

Gnomad4 OTH AF: 0.000956

Alfa AF: 0.00196 Hom.: 4066

ClinVar

Significance: Likely benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Cataract 21 multiple types Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Mendelics

May 28, 2019

- -

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Oct 01, 2024

MAF: BS2 -

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: rs5818251; hg19: chr16-79633805;