Variant chr19-464140-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_182577.3(ODF3L2):c.574G>A(p.Ala192Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000946 in 799,032 control chromosomes in the GnomAD database, including 9 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0039 ( 0 hom., cov: 0)

Exomes 𝑓: 0.00086 ( 9 hom. )

Consequence

ODF3L2
NM_182577.3 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.776

Variant links:

Genes affected

ODF3L2 (HGNC:):

ODF3L2 links:

CIMAP1D (HGNC:26841): (CIMAP1 family member D) Located in cytoplasmic microtubule. [provided by Alliance of Genome Resources, Apr 2022]

CIMAP1D 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 (MetaRNN=0.003979534).

BP6

Variant 19-464140-C-T is Benign according to our data. Variant chr19-464140-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2411977.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0778 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ODF3L2	NM_182577.3 linkuse as main transcript	c.574G>A	p.Ala192Thr	missense_variant	4/4	ENST00000315489.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CIMAP1D	ENST00000315489.5 linkuse as main transcript	c.574G>A	p.Ala192Thr	missense_variant	4/4	1	NM_182577.3	P2	Q3SX64-1
CIMAP1D	ENST00000382696.7 linkuse as main transcript	c.466G>A	p.Ala156Thr	missense_variant	3/3	1		A2	Q3SX64-2
CIMAP1D	ENST00000591681.3 linkuse as main transcript			downstream_gene_variant		2

Frequencies

GnomAD3 genomes

AF:

0.00391

AC:

AN:

23298

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000155

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00158

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.0950

Gnomad SAS

AF:

0.00163

Gnomad FIN

AF:

0.000603

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000186

Gnomad OTH

AF:

0.00

GnomAD4 exome

AF:

0.000859

AC:

666

AN:

775716

Hom.:

Cov.:

AF XY:

0.000833

AC XY:

309

AN XY:

370860

show subpopulations

Gnomad4 AFR exome

AF:

0.0000605

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.0339

Gnomad4 SAS exome

AF:

0.000658

Gnomad4 FIN exome

AF:

0.000102

Gnomad4 NFE exome

AF:

0.0000231

Gnomad4 OTH exome

AF:

0.000859

GnomAD4 genome

AF:

0.00386

AC:

AN:

23316

Hom.:

Cov.:

AF XY:

0.00413

AC XY:

AN XY:

11378

show subpopulations

Gnomad4 AFR

AF:

0.000155

Gnomad4 AMR

AF:

0.00158

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.0943

Gnomad4 SAS

AF:

0.00163

Gnomad4 FIN

AF:

0.000603

Gnomad4 NFE

AF:

0.000186

Gnomad4 OTH

AF:

0.00

Bravo

AF:

0.000933

ExAC

AF:

0.0000606

AC:

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Ambry Genetics

Aug 02, 2021

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.074

BayesDel_addAF

Benign

-0.29

BayesDel_noAF

Benign

-0.66

CADD

Benign

DANN

Uncertain

0.99

Eigen

Benign

-0.66

Eigen_PC

Benign

-0.80

FATHMM_MKL

Benign

0.078

LIST_S2

Benign

0.58

T;T

MetaRNN

Benign

0.0040

T;T

MetaSVM

Benign

-1.1

MutationTaster

Benign

1.0

N;N

PrimateAI

Benign

0.45

PROVEAN

Benign

-2.1

N;N

REVEL

Benign

0.053

Sift

Uncertain

0.013

D;D

Sift4G

Uncertain

0.021

D;D

Polyphen

0.91

P;P

Vest4

0.038

MVP

0.11

MPC

0.26

ClinPred

0.63

GERP RS

0.90

Varity_R

0.13

gMVP

0.41

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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