11-65793149-C-T

Variant names:

• chr11-65793149-C-T
• rs642803
• NM_004561.4:c.101-882C>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_004561.4(OVOL1):​c.101-882C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.421 in 152,094 control chromosomes in the GnomAD database, including 14,100 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 0.42 (14100 hom., cov: 33)
• Consequence: OVOL1 NM_004561.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05

Genes affected

OVOL1 (HGNC:8525): (ovo like transcriptional repressor 1) This gene encodes a putative zinc finger containing transcription factor that is highly similar to homologous protein in Drosophila and mouse. Based on known functions in these species, this protein is likely involved in hair formation and spermatogenesis in human as well. [provided by RefSeq, Aug 2011]

LOC124902693 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.546 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OVOL1	NM_004561.4	c.101-882C>T		intron_variant	Intron 1 of 3	ENST00000335987.8	NP_004552.2
LOC124902693	XM_047427980.1	c.*1162-762G>A		intron_variant	Intron 4 of 6		XP_047283936.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OVOL1	ENST00000335987.8	c.101-882C>T		intron_variant	Intron 1 of 3	1	NM_004561.4	ENSP00000337862.3
OVOL1	ENST00000531907.1	n.493+699C>T		intron_variant	Intron 2 of 2	4

Frequencies

GnomAD3 genomes AF: 0.422 AC: 64076 AN: 151974 Hom.: 14106 Cov.: 33

Gnomad AFR AF: 0.312

Gnomad AMI AF: 0.622

Gnomad AMR AF: 0.547

Gnomad ASJ AF: 0.446

Gnomad EAS AF: 0.415

Gnomad SAS AF: 0.564

Gnomad FIN AF: 0.365

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.455

Gnomad OTH AF: 0.435

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

GnomAD4 genome AF: 0.421 AC: 64103 AN: 152094 Hom.: 14100 Cov.: 33 AF XY: 0.421 AC XY: 31321 AN XY: 74330

Gnomad4 AFR AF: 0.312

Gnomad4 AMR AF: 0.547

Gnomad4 ASJ AF: 0.446

Gnomad4 EAS AF: 0.416

Gnomad4 SAS AF: 0.563

Gnomad4 FIN AF: 0.365

Gnomad4 NFE AF: 0.455

Gnomad4 OTH AF: 0.435

Alfa AF: 0.448 Hom.: 18586

Bravo AF: 0.434

Asia WGS AF: 0.516 AC: 1797 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.30
DANN	Benign	0.49

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

Other links and lift over

dbSNP: rs642803; hg19: chr11-65560620;