rs4931434

chr12-31113353-C-A

Variant summary

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

The NR_153414.1(OVOS2):n.5465-270G>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 0.405 in 151,838 control chromosomes in the GnomAD database, including 13,007 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 0.41 (13007 hom., cov: 32)
• Consequence: OVOS2 NR_153414.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.753 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
OVOS2	NR_153414.1	n.5465-270G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000641844.2	n.5678-270G>T		intron_variant, non_coding_transcript_variant
	ENST00000702253.1	n.606-270G>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.405 AC: 61440 AN: 151720 Hom.: 12975 Cov.: 32

Gnomad AFR AF: 0.484

Gnomad AMI AF: 0.364

Gnomad AMR AF: 0.508

Gnomad ASJ AF: 0.295

Gnomad EAS AF: 0.773

Gnomad SAS AF: 0.408

Gnomad FIN AF: 0.327

Gnomad MID AF: 0.229

Gnomad NFE AF: 0.325

Gnomad OTH AF: 0.381

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

GnomAD4 genome AF: 0.405 AC: 61518 AN: 151838 Hom.: 13007 Cov.: 32 AF XY: 0.409 AC XY: 30335 AN XY: 74202

Gnomad4 AFR AF: 0.484

Gnomad4 AMR AF: 0.509

Gnomad4 ASJ AF: 0.295

Gnomad4 EAS AF: 0.773

Gnomad4 SAS AF: 0.408

Gnomad4 FIN AF: 0.327

Gnomad4 NFE AF: 0.325

Gnomad4 OTH AF: 0.378

Alfa AF: 0.334 Hom.: 12048

Asia WGS AF: 0.566 AC: 1965 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	0.59
Dann	Benign	0.70

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: rs4931434; hg19: chr12-31266287;