Variant 16-4797168-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_024589.3(ROGDI):c.*292C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.428 in 365,080 control chromosomes in the GnomAD database, including 35,247 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.41 ( 13638 hom., cov: 31)

Exomes 𝑓: 0.44 ( 21609 hom. )

Consequence

ROGDI
NM_024589.3 3_prime_UTR

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.544

Variant links:

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 links:

ROGDI (HGNC:):

ROGDI links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.68).

BP6

Variant 16-4797168-G-A is Benign according to our data. Variant chr16-4797168-G-A is described in ClinVar as [Benign]. Clinvar id is 319394.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.506 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons	MANE	Protein	UniProt
ROGDI	NM_024589.3 linkuse as main transcript	c.*292C>T	3_prime_UTR_variant	11/11	ENST00000322048.12	NP_078865.1	Q9GZN7
ROGDI	XM_006720947.5 linkuse as main transcript	c.*292C>T	3_prime_UTR_variant	11/11		XP_006721010.1
ROGDI	XM_047434636.1 linkuse as main transcript	c.*292C>T	3_prime_UTR_variant	9/9		XP_047290592.1
ROGDI	NR_046480.2 linkuse as main transcript	n.1163C>T	non_coding_transcript_exon_variant	10/10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ROGDI	ENST00000322048 linkuse as main transcript	c.*292C>T		3_prime_UTR_variant	11/11	1	NM_024589.3	ENSP00000322832.6		Q9GZN7

Frequencies

GnomAD3 genomes

AF:

0.410

AC:

62251

AN:

151700

Hom.:

13628

Cov.:

show subpopulations

Gnomad AFR

AF:

0.247

Gnomad AMI

AF:

0.387

Gnomad AMR

AF:

0.515

Gnomad ASJ

AF:

0.489

Gnomad EAS

AF:

0.344

Gnomad SAS

AF:

0.498

Gnomad FIN

AF:

0.445

Gnomad MID

AF:

0.440

Gnomad NFE

AF:

0.475

Gnomad OTH

AF:

0.436

GnomAD4 exome

AF:

0.441

AC:

94142

AN:

213262

Hom.:

21609

Cov.:

AF XY:

0.447

AC XY:

50019

AN XY:

111876

show subpopulations

Gnomad4 AFR exome

AF:

0.225

Gnomad4 AMR exome

AF:

0.540

Gnomad4 ASJ exome

AF:

0.466

Gnomad4 EAS exome

AF:

0.325

Gnomad4 SAS exome

AF:

0.484

Gnomad4 FIN exome

AF:

0.413

Gnomad4 NFE exome

AF:

0.454

Gnomad4 OTH exome

AF:

0.439

GnomAD4 genome

AF:

0.410

AC:

62283

AN:

151818

Hom.:

13638

Cov.:

AF XY:

0.413

AC XY:

30603

AN XY:

74184

show subpopulations

Gnomad4 AFR

AF:

0.247

Gnomad4 AMR

AF:

0.516

Gnomad4 ASJ

AF:

0.489

Gnomad4 EAS

AF:

0.343

Gnomad4 SAS

AF:

0.496

Gnomad4 FIN

AF:

0.445

Gnomad4 NFE

AF:

0.475

Gnomad4 OTH

AF:

0.442

Alfa

AF:

0.465

Hom.:

15741

Bravo

AF:

0.408

Asia WGS

AF:

0.476

AC:

1655

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

Amelocerebrohypohidrotic syndrome

Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Apr 27, 2017

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases was too high to be consistent with this variant causing disease. Therefore, this variant is classified as benign. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.68

CADD

Benign

DANN

Benign

0.84

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over