rs17804971

Variant names:

• chr12-9467109-C-T
• rs17804971
• ENST00000641304.1:n.492+5675C>T

Variant summary

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

The ENST00000641304.1(ENSG00000284634):​n.492+5675C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.538 in 151,582 control chromosomes in the GnomAD database, including 22,115 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 0.54 (22115 hom., cov: 30)
• Consequence: ENSG00000284634 ENST00000641304.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.730
• Publications: 9 publications found

Genes affected

ENSG00000284634 (HGNC:):

OVOS1P (HGNC:34045):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.579 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OVOS1P	NR_153413.2	n.703+5675C>T		intron_variant	Intron 2 of 45

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000284634	ENST00000641304.1	n.492+5675C>T		intron_variant	Intron 2 of 9
ENSG00000284634	ENST00000641608.1	n.695+5675C>T		intron_variant	Intron 2 of 5
ENSG00000284634	ENST00000733152.1	n.1008+5675C>T		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.538 AC: 81513 AN: 151468 Hom.: 22102 Cov.: 30

Gnomad AFR AF: 0.504

Gnomad AMI AF: 0.611

Gnomad AMR AF: 0.491

Gnomad ASJ AF: 0.539

Gnomad EAS AF: 0.458

Gnomad SAS AF: 0.530

Gnomad FIN AF: 0.484

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.584

Gnomad OTH AF: 0.516

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

GnomAD4 genome AF: 0.538 AC: 81569 AN: 151582 Hom.: 22115 Cov.: 30 AF XY: 0.533 AC XY: 39463 AN XY: 74074

African (AFR) AF: 0.504 AC: 20796 AN: 41278

American (AMR) AF: 0.491 AC: 7495 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.539 AC: 1867 AN: 3464

East Asian (EAS) AF: 0.457 AC: 2329 AN: 5096

South Asian (SAS) AF: 0.530 AC: 2542 AN: 4796

European-Finnish (FIN) AF: 0.484 AC: 5101 AN: 10530

Middle Eastern (MID) AF: 0.517 AC: 151 AN: 292

European-Non Finnish (NFE) AF: 0.584 AC: 39643 AN: 67856

Other (OTH) AF: 0.519 AC: 1088 AN: 2098

Alfa AF: 0.554 Hom.: 3991

Bravo AF: 0.537

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.85
DANN	Benign	0.37
PhyloP100		-0.73

Splicing

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

Other links and lift over

dbSNP: rs17804971; hg19: chr12-9619705;