Variant chr4-70196539-C-T 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_017855.4(ODAM):c.-5C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.269 in 1,539,130 control chromosomes in the GnomAD database, including 60,627 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.25 ( 5151 hom., cov: 32)

Exomes 𝑓: 0.27 ( 55476 hom. )

Consequence

ODAM
NM_017855.4 5_prime_UTR

Scores

Clinical Significance

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

Conservation

PhyloP100: 2.00

Variant links:

Genes affected

ODAM (HGNC:26043): (odontogenic, ameloblast associated) Involved in several processes, including positive regulation of GTPase activity; positive regulation of epithelial cell proliferation involved in wound healing; and positive regulation of macromolecule metabolic process. Located in several cellular components, including extracellular space; mitotic spindle; and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ODAM 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=-0.48).

BP6

Variant 4-70196539-C-T is Benign according to our data. Variant chr4-70196539-C-T is described in ClinVar as [Benign]. Clinvar id is 1326082.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.456 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ODAM	NM_017855.4 linkuse as main transcript	c.-5C>T		5_prime_UTR_variant	2/12	ENST00000683306.1

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Appris
ODAM	ENST00000683306.1 linkuse as main transcript	c.-5C>T	5_prime_UTR_variant	2/12		NM_017855.4	P1
ODAM	ENST00000396094.6 linkuse as main transcript	c.-5C>T	5_prime_UTR_variant	1/11	5		P1
ODAM	ENST00000510709.6 linkuse as main transcript	c.-5C>T	5_prime_UTR_variant	1/8	5

Frequencies

GnomAD3 genomes

AF:

0.249

AC:

37757

AN:

151536

Hom.:

5144

Cov.:

show subpopulations

Gnomad AFR

AF:

0.174

Gnomad AMI

AF:

0.203

Gnomad AMR

AF:

0.217

Gnomad ASJ

AF:

0.424

Gnomad EAS

AF:

0.285

Gnomad SAS

AF:

0.472

Gnomad FIN

AF:

0.223

Gnomad MID

AF:

0.367

Gnomad NFE

AF:

0.278

Gnomad OTH

AF:

0.286

GnomAD3 exomes

AF:

0.260

AC:

56245

AN:

216450

Hom.:

8453

AF XY:

0.276

AC XY:

32165

AN XY:

116652

show subpopulations

Gnomad AFR exome

AF:

0.159

Gnomad AMR exome

AF:

0.133

Gnomad ASJ exome

AF:

0.399

Gnomad EAS exome

AF:

0.248

Gnomad SAS exome

AF:

0.462

Gnomad FIN exome

AF:

0.223

Gnomad NFE exome

AF:

0.257

Gnomad OTH exome

AF:

0.289

GnomAD4 exome

AF:

0.271

AC:

376103

AN:

1387476

Hom.:

55476

Cov.:

AF XY:

0.279

AC XY:

192463

AN XY:

690370

show subpopulations

Gnomad4 AFR exome

AF:

0.163

Gnomad4 AMR exome

AF:

0.144

Gnomad4 ASJ exome

AF:

0.405

Gnomad4 EAS exome

AF:

0.309

Gnomad4 SAS exome

AF:

0.466

Gnomad4 FIN exome

AF:

0.233

Gnomad4 NFE exome

AF:

0.261

Gnomad4 OTH exome

AF:

0.286

GnomAD4 genome

AF:

0.249

AC:

37787

AN:

151654

Hom.:

5151

Cov.:

AF XY:

0.251

AC XY:

18581

AN XY:

74090

show subpopulations

Gnomad4 AFR

AF:

0.174

Gnomad4 AMR

AF:

0.217

Gnomad4 ASJ

AF:

0.424

Gnomad4 EAS

AF:

0.285

Gnomad4 SAS

AF:

0.472

Gnomad4 FIN

AF:

0.223

Gnomad4 NFE

AF:

0.278

Gnomad4 OTH

AF:

0.293

Alfa

AF:

0.278

Hom.:

3163

Bravo

AF:

0.239

Asia WGS

AF:

0.332

AC:

1151

AN:

3470

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Nov 16, 2021	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.48

CADD

Benign

DANN

Benign

0.70

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