Variant 1-86358813-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2

The NM_001366781.1(ODF2L):c.1246A>G(p.Lys416Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00324 in 1,500,070 control chromosomes in the GnomAD database, including 8 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 Benign (★★).

Frequency

Genomes: 𝑓 0.0029 ( 1 hom., cov: 32)

Exomes 𝑓: 0.0033 ( 7 hom. )

Consequence

ODF2L
NM_001366781.1 missense

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.681

Variant links:

Genes affected

ODF2L (HGNC:29225): (outer dense fiber of sperm tails 2 like) Involved in negative regulation of cilium assembly. Located in centriolar satellite and ciliary basal body. [provided by Alliance of Genome Resources, Apr 2022]

ODF2L links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.004457921).

BP6

Variant 1-86358813-T-C is Benign according to our data. Variant chr1-86358813-T-C is described in ClinVar as [Benign]. Clinvar id is 791082.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS2

High Homozygotes in GnomAdExome4 at 7 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ODF2L	NM_001366781.1 link	c.1246A>G	p.Lys416Glu	missense_variant	12/17	ENST00000460698.7	NP_001353710.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ODF2L	ENST00000460698.7 link	c.1246A>G	p.Lys416Glu	missense_variant	12/17	5	NM_001366781.1	ENSP00000433092.2		Q9ULJ1-4H0YD68

Frequencies

GnomAD3 genomes

AF:

0.00288

AC:

438

AN:

152174

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000868

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00864

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000207

Gnomad FIN

AF:

0.00104

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.00365

Gnomad OTH

AF:

0.00382

GnomAD3 exomes

AF:

0.00251

AC:

527

AN:

210188

Hom.:

AF XY:

0.00225

AC XY:

257

AN XY:

114238

show subpopulations

Gnomad AFR exome

AF:

0.000870

Gnomad AMR exome

AF:

0.00631

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.000530

Gnomad NFE exome

AF:

0.00325

Gnomad OTH exome

AF:

0.00442

GnomAD4 exome

AF:

0.00328

AC:

4416

AN:

1347778

Hom.:

Cov.:

AF XY:

0.00317

AC XY:

2130

AN XY:

671400

show subpopulations

Gnomad4 AFR exome

AF:

0.000701

Gnomad4 AMR exome

AF:

0.00601

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.0000139

Gnomad4 FIN exome

AF:

0.000370

Gnomad4 NFE exome

AF:

0.00387

Gnomad4 OTH exome

AF:

0.00266

GnomAD4 genome

AF:

0.00288

AC:

438

AN:

152292

Hom.:

Cov.:

AF XY:

0.00278

AC XY:

207

AN XY:

74478

show subpopulations

Gnomad4 AFR

AF:

0.000866

Gnomad4 AMR

AF:

0.00863

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000207

Gnomad4 FIN

AF:

0.00104

Gnomad4 NFE

AF:

0.00365

Gnomad4 OTH

AF:

0.00378

Alfa

AF:

0.00286

Hom.:

Bravo

AF:

0.00320

TwinsUK

AF:

0.00405

AC:

ALSPAC

AF:

0.00493

AC:

ESP6500AA

AF:

0.00114

AC:

ESP6500EA

AF:

0.00305

AC:

ExAC

AF:

0.00236

AC:

286

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	Labcorp Genetics (formerly Invitae), Labcorp	Aug 30, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.066

BayesDel_addAF

Benign

-0.34

BayesDel_noAF

Benign

-0.26

CADD

Benign

9.4

DANN

Uncertain

0.99

DEOGEN2

Benign

0.0046

T;T;.;.;T

Eigen

Benign

-0.55

Eigen_PC

Benign

-0.37

FATHMM_MKL

Benign

0.50

LIST_S2

Benign

0.57

.;T;T;T;T

MetaRNN

Benign

0.0045

T;T;T;T;T

MetaSVM

Benign

-0.99

MutationAssessor

Benign

0.49

N;.;.;.;N

PrimateAI

Benign

0.34

PROVEAN

Benign

0.63

N;N;N;N;N

REVEL

Benign

0.092

Sift

Benign

1.0

T;T;T;T;T

Sift4G

Uncertain

0.040

D;D;T;D;D

Polyphen

0.012

B;.;.;B;B

Vest4

0.19

MVP

0.35

MPC

0.010

ClinPred

0.010

GERP RS

1.9

Varity_R

0.036

gMVP

0.037

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