chr8-102560795-AGCCCCTGC-A

Position:

• chr8-102560795-AGCCCCTGC-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_024410.4(ODF1):​c.665_672delGCCCCTGC​(p.Ser222fs) variant causes a frameshift change. The variant allele was found at a frequency of 0.0289 in 898,612 control chromosomes in the GnomAD database, including 2,769 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.11 (1481 hom., cov: 20)
  • Exomes 𝑓: 0.018 (1288 hom.)
• Consequence: ODF1 NM_024410.4 frameshift
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 3.61

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]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 8-102560795-AGCCCCTGC-A is Benign according to our data. Variant chr8-102560795-AGCCCCTGC-A is described in ClinVar as [Benign]. Clinvar id is 776368.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.321 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ODF1	NM_024410.4	c.665_672delGCCCCTGC	p.Ser222fs	frameshift_variant	2/2	ENST00000285402.4	NP_077721.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ODF1	ENST00000285402.4	c.665_672delGCCCCTGC	p.Ser222fs	frameshift_variant	2/2	1	NM_024410.4	ENSP00000285402.3
ODF1	ENST00000518835.1	c.44_51delGCCCCTGC	p.Ser15fs	frameshift_variant	2/2	3		ENSP00000430023.1

Frequencies

GnomAD3 genomes AF: 0.114 AC: 11929 AN: 104846 Hom.: 1470 Cov.: 20

Gnomad AFR AF: 0.326

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0550

Gnomad ASJ AF: 0.00309

Gnomad EAS AF: 0.0242

Gnomad SAS AF: 0.00242

Gnomad FIN AF: 0.00192

Gnomad MID AF: 0.0442

Gnomad NFE AF: 0.00727

Gnomad OTH AF: 0.0850

GnomAD4 exome AF: 0.0176 AC: 13949 AN: 793640 Hom.: 1288 AF XY: 0.0159 AC XY: 6229 AN XY: 392740

Gnomad4 AFR exome AF: 0.339

Gnomad4 AMR exome AF: 0.0402

Gnomad4 ASJ exome AF: 0.00473

Gnomad4 EAS exome AF: 0.0308

Gnomad4 SAS exome AF: 0.00417

Gnomad4 FIN exome AF: 0.00250

Gnomad4 NFE exome AF: 0.00525

Gnomad4 OTH exome AF: 0.0350

GnomAD4 genome AF: 0.114 AC: 11983 AN: 104972 Hom.: 1481 Cov.: 20 AF XY: 0.110 AC XY: 5623 AN XY: 51044

Gnomad4 AFR AF: 0.327

Gnomad4 AMR AF: 0.0547

Gnomad4 ASJ AF: 0.00309

Gnomad4 EAS AF: 0.0245

Gnomad4 SAS AF: 0.00244

Gnomad4 FIN AF: 0.00192

Gnomad4 NFE AF: 0.00727

Gnomad4 OTH AF: 0.0838

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Aug 20, 2018

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Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs763278818; hg19: chr8-103573023; COSMIC: COSV53433126;