rs786205125

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr16-4802482-GGCCCCGCC-G
• chr16-4802482-GGCCCCGCC-GGCCCCGCCGCCCCGCC

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_024589.3(ROGDI):​c.45+37_46-30delGGCGGGGC variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000155 in 1,223,782 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.000020 (0 hom., cov: 33)
  • Exomes 𝑓: 0.000015 (0 hom.)
• Consequence: ROGDI NM_024589.3 intron
• Clinical Significance: Benign criteria provided, single submitter P:1 B:1
• Conservation: PhyloP100: 0.554

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]

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ROGDI	NM_024589.3	c.45+37_46-30delGGCGGGGC		intron_variant	Intron 1 of 10	ENST00000322048.12	NP_078865.1
ROGDI	XM_006720947.5	c.45+37_46-30delGGCGGGGC		intron_variant	Intron 1 of 10		XP_006721010.1
ROGDI	NR_046480.2	n.107+37_108-30delGGCGGGGC		intron_variant	Intron 1 of 9
ROGDI	XM_047434636.1	c.-207_-200delGGCGGGGC		upstream_gene_variant			XP_047290592.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ROGDI	ENST00000322048.12	c.45+37_46-30delGGCGGGGC		intron_variant	Intron 1 of 10	1	NM_024589.3	ENSP00000322832.6

Frequencies

GnomAD3 genomes AF: 0.0000133 AC: 2 AN: 150306 Hom.: 0 Cov.: 33

Gnomad AFR AF: 0.0000242

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

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: 0.0000149

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.0000149 AC: 16 AN: 1073368 Hom.: 0 AF XY: 0.00000978 AC XY: 5 AN XY: 511294

Gnomad4 AFR exome AF: 0.0000453

Gnomad4 AMR exome AF: 0.000131

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.0000404

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0000131

Gnomad4 OTH exome AF: 0.0000236

GnomAD4 genome AF: 0.0000199 AC: 3 AN: 150414 Hom.: 0 Cov.: 33 AF XY: 0.0000272 AC XY: 2 AN XY: 73416

Gnomad4 AFR AF: 0.0000484

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000149

Gnomad4 OTH AF: 0.00

Bravo AF: 0.0000189

ClinVar

Significance: Benign

Submissions summary: Pathogenic:1 Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Amelocerebrohypohidrotic syndrome Pathogenic:1 Benign:1

Aug 09, 2022

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Feb 01, 2013

OMIM

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: literature only

- -

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: rs786205125; hg19: chr16-4852483;