Variant 8-102560773-C-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_024410.4(ODF1):c.642C>G(p.Pro214Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.61 in 1,608,142 control chromosomes in the GnomAD database, including 302,559 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.58 ( 25206 hom., cov: 30)

Exomes 𝑓: 0.61 ( 277353 hom. )

Consequence

ODF1
NM_024410.4 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.578

Variant links:

Genes affected

ODF1 (HGNC:8113): (outer dense fiber of sperm tails 1) The outer dense fibers are cytoskeletal structures that surround the axoneme in the middle piece and principal piece of the sperm tail. The fibers function in maintaining the elastic structure and recoil of the sperm tail as well as in protecting the tail from shear forces during epididymal transport and ejaculation. Defects in the outer dense fibers lead to abnormal sperm morphology and infertility. The human outer dense fibers contains at least 10 major proteins and this gene encodes the main protein. [provided by RefSeq, Jul 2008]

ODF1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.48).

BP6

Variant 8-102560773-C-G is Benign according to our data. Variant chr8-102560773-C-G is described in ClinVar as [Benign]. Clinvar id is 768252.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.578 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.641 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ODF1	NM_024410.4 linkuse as main transcript	c.642C>G	p.Pro214Pro	synonymous_variant	2/2	ENST00000285402.4	NP_077721.2	Q14990

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ODF1	ENST00000285402.4 linkuse as main transcript	c.642C>G	p.Pro214Pro	synonymous_variant	2/2	1	NM_024410.4	ENSP00000285402.3		Q14990
ODF1	ENST00000518835.1 linkuse as main transcript	c.21C>G	p.Pro7Pro	synonymous_variant	2/2	3		ENSP00000430023.1		E5RH17

Frequencies

GnomAD3 genomes

AF:

0.580

AC:

86130

AN:

148612

Hom.:

25184

Cov.:

show subpopulations

Gnomad AFR

AF:

0.470

Gnomad AMI

AF:

0.610

Gnomad AMR

AF:

0.569

Gnomad ASJ

AF:

0.742

Gnomad EAS

AF:

0.335

Gnomad SAS

AF:

0.576

Gnomad FIN

AF:

0.635

Gnomad MID

AF:

0.732

Gnomad NFE

AF:

0.646

Gnomad OTH

AF:

0.610

GnomAD3 exomes

AF:

0.647

AC:

146215

AN:

226018

Hom.:

44014

AF XY:

0.653

AC XY:

79850

AN XY:

122290

show subpopulations

Gnomad AFR exome

AF:

0.534

Gnomad AMR exome

AF:

0.617

Gnomad ASJ exome

AF:

0.772

Gnomad EAS exome

AF:

0.387

Gnomad SAS exome

AF:

0.653

Gnomad FIN exome

AF:

0.668

Gnomad NFE exome

AF:

0.689

Gnomad OTH exome

AF:

0.690

GnomAD4 exome

AF:

0.613

AC:

895115

AN:

1459432

Hom.:

277353

Cov.:

AF XY:

0.614

AC XY:

445610

AN XY:

726122

show subpopulations

Gnomad4 AFR exome

AF:

0.468

Gnomad4 AMR exome

AF:

0.531

Gnomad4 ASJ exome

AF:

0.736

Gnomad4 EAS exome

AF:

0.350

Gnomad4 SAS exome

AF:

0.566

Gnomad4 FIN exome

AF:

0.620

Gnomad4 NFE exome

AF:

0.630

Gnomad4 OTH exome

AF:

0.610

GnomAD4 genome

AF:

0.580

AC:

86188

AN:

148710

Hom.:

25206

Cov.:

AF XY:

0.576

AC XY:

41891

AN XY:

72696

show subpopulations

Gnomad4 AFR

AF:

0.470

Gnomad4 AMR

AF:

0.570

Gnomad4 ASJ

AF:

0.742

Gnomad4 EAS

AF:

0.335

Gnomad4 SAS

AF:

0.576

Gnomad4 FIN

AF:

0.635

Gnomad4 NFE

AF:

0.646

Gnomad4 OTH

AF:

0.613

Alfa

AF:

0.479

Hom.:

1355

Bravo

AF:

0.558

Asia WGS

AF:

0.516

AC:

1791

AN:

3474

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 20, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.48

CADD

Benign

1.9

DANN

Benign

0.59

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