rs113858060

Variant names:

• chr16-4802372-G-A
• rs113858060
• NM_024589.3:c.117+10C>T

Your query was ambiguous. Multiple possible variants found:

• chr16-4802372-G-A
• chr16-4802372-G-C
• chr16-4802372-G-T

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BS1 BS2

The NM_024589.3(ROGDI):​c.117+10C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00122 in 1,566,322 control chromosomes in the GnomAD database, including 26 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.0067 (9 hom., cov: 33)
  • Exomes 𝑓: 0.00063 (17 hom.)
• Consequence: ROGDI NM_024589.3 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.306
• 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: Benign. The variant received -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BP6: Variant 16-4802372-G-A is Benign according to our data. Variant chr16-4802372-G-A is described in ClinVar as [Benign]. Clinvar id is 416248.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.00674 (1026/152242) while in subpopulation AFR AF = 0.0235 (976/41572). AF 95% confidence interval is 0.0223. There are 9 homozygotes in GnomAd4. There are 443 alleles in the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 9 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ROGDI	NM_024589.3	c.117+10C>T		intron_variant	Intron 2 of 10	ENST00000322048.12	NP_078865.1
ROGDI	NR_046480.2	n.179+10C>T		intron_variant	Intron 2 of 9
ROGDI	XM_006720947.5	c.117+10C>T		intron_variant	Intron 2 of 10		XP_006721010.1
ROGDI	XM_047434636.1	c.-99+10C>T		intron_variant	Intron 1 of 8		XP_047290592.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ROGDI	ENST00000322048.12	c.117+10C>T		intron_variant	Intron 2 of 10	1	NM_024589.3	ENSP00000322832.6

Frequencies

GnomAD3 genomes AF: 0.00674 AC: 1025 AN: 152124 Hom.: 9 Cov.: 33

Gnomad AFR AF: 0.0235

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00249

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: 0.0000294

Gnomad OTH AF: 0.00479

GnomAD2 exomes AF: 0.00168 AC: 299 AN: 178084 AF XY: 0.00122

Gnomad AFR exome AF: 0.0235

Gnomad AMR exome AF: 0.00116

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000520

Gnomad OTH exome AF: 0.000872

GnomAD4 exome AF: 0.000627 AC: 886 AN: 1414080 Hom.: 17 Cov.: 31 AF XY: 0.000555 AC XY: 389 AN XY: 701446

African (AFR) AF: 0.0233 AC: 739 AN: 31706

American (AMR) AF: 0.00125 AC: 47 AN: 37520

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 24510

East Asian (EAS) AF: 0.00 AC: 0 AN: 37504

South Asian (SAS) AF: 0.0000374 AC: 3 AN: 80256

European-Finnish (FIN) AF: 0.0000215 AC: 1 AN: 46430

Middle Eastern (MID) AF: 0.000537 AC: 3 AN: 5584

European-Non Finnish (NFE) AF: 0.0000174 AC: 19 AN: 1092208

Other (OTH) AF: 0.00127 AC: 74 AN: 58362

GnomAD4 genome AF: 0.00674 AC: 1026 AN: 152242 Hom.: 9 Cov.: 33 AF XY: 0.00595 AC XY: 443 AN XY: 74446

African (AFR) AF: 0.0235 AC: 976 AN: 41572

American (AMR) AF: 0.00248 AC: 38 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5160

South Asian (SAS) AF: 0.00 AC: 0 AN: 4828

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10596

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 292

European-Non Finnish (NFE) AF: 0.0000294 AC: 2 AN: 67996

Other (OTH) AF: 0.00474 AC: 10 AN: 2110

Alfa AF: 0.000181 Hom.: 0

Bravo AF: 0.00755

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:1

Nov 20, 2017

Athena Diagnostics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Amelocerebrohypohidrotic syndrome Benign:1

Feb 02, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	4.0
DANN	Benign	0.85
PhyloP100		-0.31
PromoterAI		0.00030	Neutral
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0
Mutation Taster		=100/0	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs113858060; hg19: chr16-4852373;