chr16-79319284-T-A

Position:

• chr16-79319284-T-A

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4 BA1

The XM_024450279.2(MAF):​c.*29-106383A>T variant causes a intron change. The variant allele was found at a frequency of 0.583 in 152,078 control chromosomes in the GnomAD database, including 28,360 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.58 (28360 hom., cov: 33)
• Consequence: MAF XM_024450279.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.60

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -9 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.13).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.716 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MAF	XM_024450279.2	c.*29-106383A>T		intron_variant			XP_024306047.1
		n.79319284T>A		intergenic_region
MAF	XR_001751902.3	n.2016-106383A>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.584 AC: 88716 AN: 151960 Hom.: 28356 Cov.: 33

Gnomad AFR AF: 0.294

Gnomad AMI AF: 0.714

Gnomad AMR AF: 0.695

Gnomad ASJ AF: 0.546

Gnomad EAS AF: 0.717

Gnomad SAS AF: 0.736

Gnomad FIN AF: 0.733

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.690

Gnomad OTH AF: 0.612

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.583 AC: 88736 AN: 152078 Hom.: 28360 Cov.: 33 AF XY: 0.593 AC XY: 44104 AN XY: 74344

Gnomad4 AFR AF: 0.294

Gnomad4 AMR AF: 0.696

Gnomad4 ASJ AF: 0.546

Gnomad4 EAS AF: 0.718

Gnomad4 SAS AF: 0.736

Gnomad4 FIN AF: 0.733

Gnomad4 NFE AF: 0.690

Gnomad4 OTH AF: 0.606

Alfa AF: 0.512 Hom.: 1639

Bravo AF: 0.567

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.13
CADD	Benign	16
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1509309; hg19: chr16-79353181;