Variant 16-4797080-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_024589.3(ROGDI):c.*380G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0429 in 244,836 control chromosomes in the GnomAD database, including 232 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.045 ( 146 hom., cov: 32)

Exomes 𝑓: 0.039 ( 86 hom. )

Consequence

ROGDI
NM_024589.3 3_prime_UTR

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.23

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BP6

Variant 16-4797080-C-T is Benign according to our data. Variant chr16-4797080-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 319391.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0529 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons	MANE
ROGDI	NM_024589.3 linkuse as main transcript	c.*380G>A	3_prime_UTR_variant	11/11	ENST00000322048.12
ROGDI	XM_006720947.5 linkuse as main transcript	c.*380G>A	3_prime_UTR_variant	11/11
ROGDI	XM_047434636.1 linkuse as main transcript	c.*380G>A	3_prime_UTR_variant	9/9
ROGDI	NR_046480.2 linkuse as main transcript	n.1251G>A	non_coding_transcript_exon_variant	10/10

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Appris
ROGDI	ENST00000322048.12 linkuse as main transcript	c.*380G>A	3_prime_UTR_variant	11/11	1	NM_024589.3	P1
ROGDI	ENST00000591292.5 linkuse as main transcript	n.2573G>A	non_coding_transcript_exon_variant	7/7	2
ROGDI	ENST00000587377.5 linkuse as main transcript	c.*564G>A	3_prime_UTR_variant, NMD_transcript_variant	11/11	5
ROGDI	ENST00000587843.5 linkuse as main transcript	c.*982G>A	3_prime_UTR_variant, NMD_transcript_variant	10/10	2

Frequencies

GnomAD3 genomes

AF:

0.0454

AC:

6908

AN:

152134

Hom.:

146

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0396

Gnomad AMI

AF:

0.0493

Gnomad AMR

AF:

0.0418

Gnomad ASJ

AF:

0.0360

Gnomad EAS

AF:

0.00558

Gnomad SAS

AF:

0.0464

Gnomad FIN

AF:

0.0365

Gnomad MID

AF:

0.0601

Gnomad NFE

AF:

0.0544

Gnomad OTH

AF:

0.0473

GnomAD4 exome

AF:

0.0389

AC:

3598

AN:

92584

Hom.:

Cov.:

AF XY:

0.0387

AC XY:

1886

AN XY:

48698

show subpopulations

Gnomad4 AFR exome

AF:

0.0253

Gnomad4 AMR exome

AF:

0.0378

Gnomad4 ASJ exome

AF:

0.0364

Gnomad4 EAS exome

AF:

0.00377

Gnomad4 SAS exome

AF:

0.0402

Gnomad4 FIN exome

AF:

0.0257

Gnomad4 NFE exome

AF:

0.0439

Gnomad4 OTH exome

AF:

0.0379

GnomAD4 genome

AF:

0.0454

AC:

6905

AN:

152252

Hom.:

146

Cov.:

AF XY:

0.0448

AC XY:

3336

AN XY:

74446

show subpopulations

Gnomad4 AFR

AF:

0.0395

Gnomad4 AMR

AF:

0.0417

Gnomad4 ASJ

AF:

0.0360

Gnomad4 EAS

AF:

0.00559

Gnomad4 SAS

AF:

0.0460

Gnomad4 FIN

AF:

0.0365

Gnomad4 NFE

AF:

0.0544

Gnomad4 OTH

AF:

0.0468

Alfa

AF:

0.0488

Hom.:

Bravo

AF:

0.0457

Asia WGS

AF:

0.0310

AC:

108

AN:

3476

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

Amelocerebrohypohidrotic syndrome

Benign:1

Likely 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 allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

1.1

DANN

Benign

0.47

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

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