rs4931443

chr12-31125097-T-Achr12-31125097-T-G

Variant summary

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

The NR_153414.1(OVOS2):n.4867+274A>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.906 in 152,272 control chromosomes in the GnomAD database, including 62,602 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 0.91 (62602 hom., cov: 33)
• Consequence: OVOS2 NR_153414.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.565

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.925 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
OVOS2	NR_153414.1	n.4867+274A>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000641844.2	n.5207+274A>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.906 AC: 137869 AN: 152154 Hom.: 62546 Cov.: 33

Gnomad AFR AF: 0.849

Gnomad AMI AF: 0.898

Gnomad AMR AF: 0.914

Gnomad ASJ AF: 0.876

Gnomad EAS AF: 0.943

Gnomad SAS AF: 0.921

Gnomad FIN AF: 0.948

Gnomad MID AF: 0.870

Gnomad NFE AF: 0.931

Gnomad OTH AF: 0.900

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

GnomAD4 genome AF: 0.906 AC: 137980 AN: 152272 Hom.: 62602 Cov.: 33 AF XY: 0.908 AC XY: 67597 AN XY: 74454

Gnomad4 AFR AF: 0.849

Gnomad4 AMR AF: 0.914

Gnomad4 ASJ AF: 0.876

Gnomad4 EAS AF: 0.943

Gnomad4 SAS AF: 0.922

Gnomad4 FIN AF: 0.948

Gnomad4 NFE AF: 0.931

Gnomad4 OTH AF: 0.901

Alfa AF: 0.922 Hom.: 8025

Bravo AF: 0.901

Asia WGS AF: 0.935 AC: 3251 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	6.5
Dann	Benign	0.52

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: rs4931443; hg19: chr12-31278031;