rs2350531

Positions:

• chr12-29468121-G-A

Variant summary

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

The NM_001353179.2(OVCH1):​c.1962-2902C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.197 in 151,974 control chromosomes in the GnomAD database, including 3,662 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 0.20 (3662 hom., cov: 32)
• Consequence: OVCH1 NM_001353179.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.167

Genes affected

OVCH1 (HGNC:23080): (ovochymase 1) Predicted to enable metal ion binding activity and serine-type endopeptidase activity. Predicted to be involved in proteolysis. Predicted to be located in extracellular region. Predicted to be active in plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

OVCH1-AS1 (HGNC:44484): (OVCH1 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.344 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
OVCH1	NM_001353179.2	c.1962-2902C>T		intron_variant		ENST00000537054.2
OVCH1-AS1	NR_073172.1	n.561-18765G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
OVCH1	ENST00000537054.2	c.1962-2902C>T		intron_variant		3	NM_001353179.2	P1
OVCH1-AS1	ENST00000551108.2	n.561-18765G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.197 AC: 29920 AN: 151856 Hom.: 3646 Cov.: 32

Gnomad AFR AF: 0.349

Gnomad AMI AF: 0.0121

Gnomad AMR AF: 0.119

Gnomad ASJ AF: 0.171

Gnomad EAS AF: 0.0807

Gnomad SAS AF: 0.108

Gnomad FIN AF: 0.199

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.142

Gnomad OTH AF: 0.168

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

GnomAD4 genome AF: 0.197 AC: 29976 AN: 151974 Hom.: 3662 Cov.: 32 AF XY: 0.195 AC XY: 14512 AN XY: 74286

Gnomad4 AFR AF: 0.349

Gnomad4 AMR AF: 0.119

Gnomad4 ASJ AF: 0.171

Gnomad4 EAS AF: 0.0805

Gnomad4 SAS AF: 0.107

Gnomad4 FIN AF: 0.199

Gnomad4 NFE AF: 0.143

Gnomad4 OTH AF: 0.166

Alfa AF: 0.167 Hom.: 656

Bravo AF: 0.197

Asia WGS AF: 0.0920 AC: 320 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.86
DANN	Benign	0.71

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: rs2350531; hg19: chr12-29621054;