16-4802482-GGCCCCGCC-GGCCCCGCCGCCCCGCC

Variant names:

• chr16-4802482-G-GGCCCCGCC
• rs786205125
• NM_024589.3:c.45+37_46-30dupGGCGGGGC

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_024589.3(ROGDI):​c.45+37_46-30dupGGCGGGGC variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000101 in 1,223,780 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.00023 (0 hom., cov: 33)
  • Exomes 𝑓: 0.000083 (0 hom.)
• Consequence: ROGDI NM_024589.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0850
• Publications: 0 publications found

Genes affected

ROGDI (HGNC:29478): (rogdi atypical leucine zipper) Involved in brain development; neurogenesis; and odontogenesis of dentin-containing tooth. Located in nuclear envelope. Implicated in Kohlschutter-Tonz syndrome. [provided by Alliance of Genome Resources, Apr 2022]

ROGDI Gene-Disease associations (from GenCC):

• amelocerebrohypohidrotic syndrome

  Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Orphanet, G2P, ClinGen, Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024589.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ROGDI	NM_024589.3	MANE Select	c.45+37_46-30dupGGCGGGGC		intron	N/A	NP_078865.1
	ROGDI	NR_046480.2		n.107+37_108-30dupGGCGGGGC		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ROGDI	ENST00000322048.12	TSL:1 MANE Select	c.45+37_46-30dupGGCGGGGC		intron	N/A	ENSP00000322832.6
	ROGDI	ENST00000907806.1		c.45+37_46-30dupGGCGGGGC		intron	N/A	ENSP00000577865.1
	ROGDI	ENST00000912071.1		c.45+37_46-30dupGGCGGGGC		intron	N/A	ENSP00000582130.1

Frequencies

GnomAD3 genomes AF: 0.000226 AC: 34 AN: 150306 Hom.: 0 Cov.: 33

Gnomad AFR AF: 0.000655

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0000663

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000414

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000446

Gnomad OTH AF: 0.000483

GnomAD4 exome AF: 0.0000829 AC: 89 AN: 1073366 Hom.: 0 Cov.: 30 AF XY: 0.0000861 AC XY: 44 AN XY: 511294

African (AFR) AF: 0.000725 AC: 16 AN: 22078

American (AMR) AF: 0.00 AC: 0 AN: 7614

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 13142

East Asian (EAS) AF: 0.00 AC: 0 AN: 24774

South Asian (SAS) AF: 0.00 AC: 0 AN: 20800

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 21938

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2988

European-Non Finnish (NFE) AF: 0.0000774 AC: 71 AN: 917730

Other (OTH) AF: 0.0000473 AC: 2 AN: 42302

GnomAD4 genome AF: 0.000226 AC: 34 AN: 150414 Hom.: 0 Cov.: 33 AF XY: 0.000272 AC XY: 20 AN XY: 73416

African (AFR) AF: 0.000653 AC: 27 AN: 41362

American (AMR) AF: 0.0000662 AC: 1 AN: 15110

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3440

East Asian (EAS) AF: 0.00 AC: 0 AN: 5142

South Asian (SAS) AF: 0.000415 AC: 2 AN: 4824

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 9954

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 290

European-Non Finnish (NFE) AF: 0.0000446 AC: 3 AN: 67288

Other (OTH) AF: 0.000478 AC: 1 AN: 2092

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.085

Splicing

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

Other links and lift over

dbSNP: rs786205125; hg19: chr16-4852483;