rs2350531

Variant names:

• chr12-29468121-G-A
• rs2350531
• NM_001353179.2:c.1962-2902C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
OVCH1	NM_001353179.2	c.1962-2902C>T		intron_variant	Intron 16 of 25	ENST00000537054.2	NP_001340108.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OVCH1	ENST00000537054.2	c.1962-2902C>T		intron_variant	Intron 16 of 25	3	NM_001353179.2	ENSP00000445480.2
OVCH1	ENST00000318184.9	c.1857-2902C>T		intron_variant	Intron 16 of 27	1		ENSP00000326708.5

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

African (AFR) AF: 0.349 AC: 14462 AN: 41426

American (AMR) AF: 0.119 AC: 1816 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.171 AC: 593 AN: 3472

East Asian (EAS) AF: 0.0805 AC: 416 AN: 5170

South Asian (SAS) AF: 0.107 AC: 514 AN: 4816

European-Finnish (FIN) AF: 0.199 AC: 2096 AN: 10540

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.143 AC: 9689 AN: 67964

Other (OTH) AF: 0.166 AC: 351 AN: 2114

Alfa AF: 0.170 Hom.: 882

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
PhyloP100		-0.17
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2350531; hg19: chr12-29621054;