8-102556951-G-C

Variant names:

• chr8-102556951-G-C
• rs2248172
• NM_024410.4:c.321-3501G>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_024410.4(ODF1):​c.321-3501G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.838 in 152,176 control chromosomes in the GnomAD database, including 53,714 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.84 (53714 hom., cov: 31)
• Consequence: ODF1 NM_024410.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07
• Publications: 1 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.849 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024410.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ODF1	NM_024410.4	MANE Select	c.321-3501G>C		intron	N/A	NP_077721.2	Q14990

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ODF1	ENST00000285402.4	TSL:1 MANE Select	c.321-3501G>C		intron	N/A	ENSP00000285402.3	Q14990

Frequencies

GnomAD3 genomes AF: 0.838 AC: 127439 AN: 152058 Hom.: 53682 Cov.: 31

Gnomad AFR AF: 0.852

Gnomad AMI AF: 0.859

Gnomad AMR AF: 0.828

Gnomad ASJ AF: 0.903

Gnomad EAS AF: 0.537

Gnomad SAS AF: 0.733

Gnomad FIN AF: 0.861

Gnomad MID AF: 0.873

Gnomad NFE AF: 0.855

Gnomad OTH AF: 0.844

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.838 AC: 127529 AN: 152176 Hom.: 53714 Cov.: 31 AF XY: 0.832 AC XY: 61910 AN XY: 74378

African (AFR) AF: 0.852 AC: 35351 AN: 41504

American (AMR) AF: 0.828 AC: 12661 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.903 AC: 3135 AN: 3470

East Asian (EAS) AF: 0.537 AC: 2777 AN: 5176

South Asian (SAS) AF: 0.733 AC: 3536 AN: 4822

European-Finnish (FIN) AF: 0.861 AC: 9114 AN: 10580

Middle Eastern (MID) AF: 0.874 AC: 257 AN: 294

European-Non Finnish (NFE) AF: 0.855 AC: 58137 AN: 68020

Other (OTH) AF: 0.843 AC: 1781 AN: 2112

Alfa AF: 0.821 Hom.: 2570

Bravo AF: 0.840

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.13
DANN	Benign	0.40
PhyloP100		-1.1
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2248172; hg19: chr8-103569179;