rs2549513

Variant names:

• chr16-79516830-C-A
• rs2549513
• XM_024450279.2:c.*28+69050G>T

Your query was ambiguous. Multiple possible variants found:

• chr16-79516830-C-A
• chr16-79516830-C-G
• chr16-79516830-C-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_001751902.3(MAF):​n.2015+69050G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.837 in 152,170 control chromosomes in the GnomAD database, including 53,563 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 0.84 (53563 hom., cov: 32)
• Consequence: MAF XR_001751902.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.200
• Publications: 16 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), G2P, Ambry Genetics
• 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.898 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.837 AC: 127249 AN: 152052 Hom.: 53525 Cov.: 32

Gnomad AFR AF: 0.746

Gnomad AMI AF: 0.909

Gnomad AMR AF: 0.894

Gnomad ASJ AF: 0.855

Gnomad EAS AF: 0.920

Gnomad SAS AF: 0.865

Gnomad FIN AF: 0.861

Gnomad MID AF: 0.864

Gnomad NFE AF: 0.865

Gnomad OTH AF: 0.848

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

GnomAD4 genome AF: 0.837 AC: 127341 AN: 152170 Hom.: 53563 Cov.: 32 AF XY: 0.838 AC XY: 62378 AN XY: 74412

African (AFR) AF: 0.746 AC: 30950 AN: 41502

American (AMR) AF: 0.894 AC: 13675 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.855 AC: 2969 AN: 3472

East Asian (EAS) AF: 0.920 AC: 4749 AN: 5162

South Asian (SAS) AF: 0.865 AC: 4167 AN: 4820

European-Finnish (FIN) AF: 0.861 AC: 9131 AN: 10604

Middle Eastern (MID) AF: 0.864 AC: 254 AN: 294

European-Non Finnish (NFE) AF: 0.865 AC: 58820 AN: 67996

Other (OTH) AF: 0.850 AC: 1797 AN: 2114

Alfa AF: 0.857 Hom.: 168324

Bravo AF: 0.838

Asia WGS AF: 0.899 AC: 3128 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.84
DANN	Benign	0.52
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs2549513; hg19: chr16-79550727;