Variant chr4-70196591-C-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1

The NM_017855.4(ODAM):c.48C>A(p.Ala16=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.129 in 1,581,112 control chromosomes in the GnomAD database, including 15,218 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.10 ( 1111 hom., cov: 32)

Exomes 𝑓: 0.13 ( 14107 hom. )

Consequence

ODAM
NM_017855.4 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.0730

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 -19 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.27).

BP6

Variant 4-70196591-C-A is Benign according to our data. Variant chr4-70196591-C-A is described in ClinVar as [Benign]. Clinvar id is 1326056.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=0.073 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.216 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.48C>A	p.Ala16=	synonymous_variant	2/12	ENST00000683306.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris
ODAM	ENST00000683306.1 linkuse as main transcript	c.48C>A	p.Ala16=	synonymous_variant	2/12		NM_017855.4	P1
ODAM	ENST00000396094.6 linkuse as main transcript	c.48C>A	p.Ala16=	synonymous_variant	1/11	5		P1
ODAM	ENST00000510709.6 linkuse as main transcript	c.48C>A	p.Ala16=	synonymous_variant	1/8	5

Frequencies

GnomAD3 genomes

AF:

0.102

AC:

15406

AN:

151780

Hom.:

1108

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0266

Gnomad AMI

AF:

0.0868

Gnomad AMR

AF:

0.108

Gnomad ASJ

AF:

0.222

Gnomad EAS

AF:

0.0111

Gnomad SAS

AF:

0.226

Gnomad FIN

AF:

0.0853

Gnomad MID

AF:

0.206

Gnomad NFE

AF:

0.139

Gnomad OTH

AF:

0.137

GnomAD3 exomes

AF:

0.123

AC:

29843

AN:

241788

Hom.:

2391

AF XY:

0.133

AC XY:

17477

AN XY:

131090

show subpopulations

Gnomad AFR exome

AF:

0.0221

Gnomad AMR exome

AF:

0.0758

Gnomad ASJ exome

AF:

0.219

Gnomad EAS exome

AF:

0.00790

Gnomad SAS exome

AF:

0.227

Gnomad FIN exome

AF:

0.0919

Gnomad NFE exome

AF:

0.139

Gnomad OTH exome

AF:

0.153

GnomAD4 exome

AF:

0.132

AC:

188032

AN:

1429214

Hom.:

14107

Cov.:

AF XY:

0.136

AC XY:

96523

AN XY:

711710

show subpopulations

Gnomad4 AFR exome

AF:

0.0219

Gnomad4 AMR exome

AF:

0.0799

Gnomad4 ASJ exome

AF:

0.214

Gnomad4 EAS exome

AF:

0.00389

Gnomad4 SAS exome

AF:

0.223

Gnomad4 FIN exome

AF:

0.0932

Gnomad4 NFE exome

AF:

0.134

Gnomad4 OTH exome

AF:

0.136

GnomAD4 genome

AF:

0.101

AC:

15416

AN:

151898

Hom.:

1111

Cov.:

AF XY:

0.100

AC XY:

7445

AN XY:

74232

show subpopulations

Gnomad4 AFR

AF:

0.0266

Gnomad4 AMR

AF:

0.108

Gnomad4 ASJ

AF:

0.222

Gnomad4 EAS

AF:

0.0111

Gnomad4 SAS

AF:

0.227

Gnomad4 FIN

AF:

0.0853

Gnomad4 NFE

AF:

0.139

Gnomad4 OTH

AF:

0.142

Alfa

AF:

0.120

Hom.:

581

Bravo

AF:

0.0983

Asia WGS

AF:

0.120

AC:

416

AN:

3476

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

-0.27

CADD

Benign

8.6

DANN

Benign

0.68

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