rs1509309

Variant names:

• chr16-79319284-T-A
• rs1509309
• XM_024450279.2:c.*29-106383A>T

Your query was ambiguous. Multiple possible variants found:

• chr16-79319284-T-A
• chr16-79319284-T-C
• chr16-79319284-T-G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 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), Ambry Genetics, G2P
• 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 -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 rank	MANE	Protein	UniProt
MAF	XM_024450279.2	c.*29-106383A>T		intron_variant	Intron 2 of 2		XP_024306047.1
MAF	XR_001751902.3	n.2016-106383A>T		intron_variant	Intron 2 of 3
MAF	XR_002957802.2	n.2016-106383A>T		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.294 AC: 12191 AN: 41438

American (AMR) AF: 0.696 AC: 10634 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.546 AC: 1895 AN: 3470

East Asian (EAS) AF: 0.718 AC: 3710 AN: 5166

South Asian (SAS) AF: 0.736 AC: 3547 AN: 4818

European-Finnish (FIN) AF: 0.733 AC: 7760 AN: 10586

Middle Eastern (MID) AF: 0.558 AC: 164 AN: 294

European-Non Finnish (NFE) AF: 0.690 AC: 46906 AN: 67996

Other (OTH) AF: 0.606 AC: 1278 AN: 2110

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
PhyloP100		4.6

Splicing

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

Other links and lift over

dbSNP: rs1509309; hg19: chr16-79353181;