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chr16-4797316-C-T

Variant summary

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

The NM_024589.3(ROGDI):​c.*144G>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 0.428 in 716,446 control chromosomes in the GnomAD database, including 67,161 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.41 ( 13132 hom., cov: 33)
Exomes 𝑓: 0.43 ( 54029 hom. )

Consequence

ROGDI
NM_024589.3 3_prime_UTR

Scores

2

Clinical Significance

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

Conservation

PhyloP100: -0.00100
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BP6
Variant 16-4797316-C-T is Benign according to our data. Variant chr16-4797316-C-T is described in ClinVar as [Benign]. Clinvar id is 319396.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.498 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ROGDINM_024589.3 linkuse as main transcriptc.*144G>A 3_prime_UTR_variant 11/11 ENST00000322048.12
ROGDIXM_006720947.5 linkuse as main transcriptc.*144G>A 3_prime_UTR_variant 11/11
ROGDIXM_047434636.1 linkuse as main transcriptc.*144G>A 3_prime_UTR_variant 9/9
ROGDINR_046480.2 linkuse as main transcriptn.1015G>A non_coding_transcript_exon_variant 10/10

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ROGDIENST00000322048.12 linkuse as main transcriptc.*144G>A 3_prime_UTR_variant 11/111 NM_024589.3 P1

Frequencies

GnomAD3 genomes
AF:
0.406
AC:
61709
AN:
151974
Hom.:
13114
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.277
Gnomad AMI
AF:
0.335
Gnomad AMR
AF:
0.507
Gnomad ASJ
AF:
0.457
Gnomad EAS
AF:
0.344
Gnomad SAS
AF:
0.493
Gnomad FIN
AF:
0.443
Gnomad MID
AF:
0.427
Gnomad NFE
AF:
0.452
Gnomad OTH
AF:
0.424
GnomAD4 exome
AF:
0.434
AC:
244761
AN:
564354
Hom.:
54029
Cov.:
8
AF XY:
0.438
AC XY:
128245
AN XY:
293026
show subpopulations
Gnomad4 AFR exome
AF:
0.270
Gnomad4 AMR exome
AF:
0.532
Gnomad4 ASJ exome
AF:
0.447
Gnomad4 EAS exome
AF:
0.344
Gnomad4 SAS exome
AF:
0.496
Gnomad4 FIN exome
AF:
0.436
Gnomad4 NFE exome
AF:
0.434
Gnomad4 OTH exome
AF:
0.432
GnomAD4 genome
AF:
0.406
AC:
61755
AN:
152092
Hom.:
13132
Cov.:
33
AF XY:
0.409
AC XY:
30404
AN XY:
74350
show subpopulations
Gnomad4 AFR
AF:
0.277
Gnomad4 AMR
AF:
0.507
Gnomad4 ASJ
AF:
0.457
Gnomad4 EAS
AF:
0.343
Gnomad4 SAS
AF:
0.491
Gnomad4 FIN
AF:
0.443
Gnomad4 NFE
AF:
0.452
Gnomad4 OTH
AF:
0.430
Alfa
AF:
0.444
Hom.:
11262
Bravo
AF:
0.405
Asia WGS
AF:
0.477
AC:
1658
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 submitterclinical testingGeneDxMay 14, 2021- -
Amelocerebrohypohidrotic syndrome Benign:1
Benign, criteria provided, single submitterclinical testingIllumina Laboratory Services, IlluminaApr 27, 2017This 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
-0.84
CADD
Benign
4.0
DANN
Benign
0.47

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.

Other links and lift over

dbSNP: rs7546; hg19: chr16-4847317; COSMIC: COSV59021666; COSMIC: COSV59021666; API