16-79302750-T-C

Variant names:

• chr16-79302750-T-C
• rs1396702
• XM_024450279.2:c.*29-89849A>G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The XM_024450279.2(MAF):​c.*29-89849A>G variant causes a intron change. The variant allele was found at a frequency of 0.939 in 152,364 control chromosomes in the GnomAD database, including 67,212 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 0.94 (67212 hom., cov: 35)
• Consequence: MAF XM_024450279.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.70

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 Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.31).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MAF	XM_024450279.2	c.*29-89849A>G		intron_variant	Intron 2 of 2		XP_024306047.1
MAF	XR_001751902.3	n.2016-89849A>G		intron_variant	Intron 2 of 3
MAF	XR_002957802.2	n.2016-89849A>G		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.939 AC: 142987 AN: 152246 Hom.: 67163 Cov.: 35

Gnomad AFR AF: 0.943

Gnomad AMI AF: 0.976

Gnomad AMR AF: 0.937

Gnomad ASJ AF: 0.923

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.940

Gnomad FIN AF: 0.983

Gnomad MID AF: 0.924

Gnomad NFE AF: 0.927

Gnomad OTH AF: 0.926

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

GnomAD4 genome AF: 0.939 AC: 143092 AN: 152364 Hom.: 67212 Cov.: 35 AF XY: 0.943 AC XY: 70281 AN XY: 74520

Gnomad4 AFR AF: 0.943

Gnomad4 AMR AF: 0.937

Gnomad4 ASJ AF: 0.923

Gnomad4 EAS AF: 0.997

Gnomad4 SAS AF: 0.940

Gnomad4 FIN AF: 0.983

Gnomad4 NFE AF: 0.927

Gnomad4 OTH AF: 0.925

Alfa AF: 0.931 Hom.: 32948

Bravo AF: 0.937

Asia WGS AF: 0.958 AC: 3331 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.31
CADD	Benign	23
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1396702; hg19: chr16-79336647;