rs1229626204

Variant names:

• chr16-79599192-CCCGCCGCCTCCGCCG-C
• rs1229626204
• NM_005360.5:c.696_710delCGGCGGAGGCGGCGG

Your query was ambiguous. Multiple possible variants found:

• chr16-79599192-CCCGCCGCCTCCGCCG-C
• chr16-79599192-CCCGCCGCCTCCGCCG-CCCGCCGCCTCCGCCGCCGCCGCCTCCGCCG

Variant summary

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

The NM_005360.5(MAF):​c.696_710delCGGCGGAGGCGGCGG​(p.Gly233_Gly237del) variant causes a disruptive inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000318 in 1,026,632 control chromosomes in the GnomAD database, including 1 homozygotes. Variant has been reported in ClinVar as Likely benign (★★).

• Frequency:
  • Genomes: 𝑓 0.0016 (1 hom., cov: 29)
  • Exomes 𝑓: 0.00011 (0 hom.)
• Consequence: MAF NM_005360.5 disruptive_inframe_deletion
• Clinical Significance: Likely benign criteria provided, multiple submitters, no conflicts B:3
• Conservation: PhyloP100: 1.65

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 -12 ACMG points.

• BP6: Variant 16-79599192-CCCGCCGCCTCCGCCG-C is Benign according to our data. Variant chr16-79599192-CCCGCCGCCTCCGCCG-C is described in ClinVar as [Likely_benign]. Clinvar id is 474937.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BS2: High AC in GnomAd4 at 231 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MAF	NM_005360.5	c.696_710delCGGCGGAGGCGGCGG	p.Gly233_Gly237del	disruptive_inframe_deletion	Exon 1 of 2	ENST00000326043.5	NP_005351.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MAF	ENST00000326043.5	c.696_710delCGGCGGAGGCGGCGG	p.Gly233_Gly237del	disruptive_inframe_deletion	Exon 1 of 2	1	NM_005360.5	ENSP00000327048.4
MAF	ENST00000569649.1	c.696_710delCGGCGGAGGCGGCGG	p.Gly233_Gly237del	disruptive_inframe_deletion	Exon 1 of 2	5		ENSP00000455097.1
MAF	ENST00000393350.1	c.696_710delCGGCGGAGGCGGCGG	p.Gly233_Gly237del	disruptive_inframe_deletion	Exon 1 of 1	6		ENSP00000377019.1

Frequencies

GnomAD3 genomes AF: 0.00156 AC: 228 AN: 145688 Hom.: 1 Cov.: 29

Gnomad AFR AF: 0.00538

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000409

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000152

Gnomad OTH AF: 0.000995

GnomAD4 exome AF: 0.000108 AC: 95 AN: 880906 Hom.: 0 AF XY: 0.0000976 AC XY: 40 AN XY: 409964

Gnomad4 AFR exome AF: 0.00510

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.000264

GnomAD4 genome AF: 0.00159 AC: 231 AN: 145726 Hom.: 1 Cov.: 29 AF XY: 0.00164 AC XY: 116 AN XY: 70822

Gnomad4 AFR AF: 0.00545

Gnomad4 AMR AF: 0.000408

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000152

Gnomad4 OTH AF: 0.000987

Alfa AF: 0.000927 Hom.: 0

ClinVar

Significance: Likely benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Ayme-Gripp syndrome;C1857768:Cataract 21 multiple types Benign:1

Aug 31, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Inborn genetic diseases Benign:1

Apr 20, 2022

Ambry Genetics

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -

not provided Benign:1

Mar 01, 2023

CeGaT Center for Human Genetics Tuebingen

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

MAF: BS1 -

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: rs1229626204; hg19: chr16-79633089;