Variant 4-48850064-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_017830.4(OCIAD1):c.359G>A(p.Arg120Gln) variant causes a missense change. The variant allele was found at a frequency of 0.00000137 in 1,459,182 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 32)

Exomes 𝑓: 0.0000014 ( 0 hom. )

Consequence

OCIAD1
NM_017830.4 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 3.58

Variant links:

Genes affected

OCIAD1 (HGNC:16074): (OCIA domain containing 1) Predicted to be involved in several processes, including hematopoietic stem cell homeostasis; positive regulation of receptor signaling pathway via JAK-STAT; and regulation of stem cell differentiation. Located in membrane. [provided by Alliance of Genome Resources, Apr 2022]

OCIAD1 links:

OCIAD1 (HGNC:):

OCIAD1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (MetaRNN=0.16002816).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OCIAD1	NM_017830.4 linkuse as main transcript	c.359G>A	p.Arg120Gln	missense_variant	6/9	ENST00000264312.12	NP_060300.1	Q9NX40-1A0A024R9U3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OCIAD1	ENST00000264312.12 linkuse as main transcript	c.359G>A	p.Arg120Gln	missense_variant	6/9	1	NM_017830.4	ENSP00000264312.7		Q9NX40-1

Frequencies

GnomAD3 genomes

Cov.:

GnomAD3 exomes

AF:

0.00000808

AC:

AN:

247498

Hom.:

AF XY:

0.00

AC XY:

AN XY:

133696

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.0000298

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.0000549

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.00000137

AC:

AN:

1459182

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

725730

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.0000227

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

9.00e-7

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

Cov.:

ExAC

AF:

0.00000824

AC:

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Jan 30, 2024

The c.374G>A (p.R125Q) alteration is located in exon 6 (coding exon 6) of the OCIAD1 gene. This alteration results from a G to A substitution at nucleotide position 374, causing the arginine (R) at amino acid position 125 to be replaced by a glutamine (Q). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.077

BayesDel_addAF

Benign

-0.28

BayesDel_noAF

Benign

-0.47

CADD

Benign

DANN

Uncertain

0.99

DEOGEN2

Benign

0.0049

T;.;T;.;T;T;T;.;T;.;T;.;.;T;T

Eigen

Benign

-0.24

Eigen_PC

Benign

-0.16

FATHMM_MKL

Benign

0.11

LIST_S2

Uncertain

0.87

D;D;.;D;D;D;.;.;D;D;D;D;D;.;D

M_CAP

Benign

0.011

MetaRNN

Benign

0.16

T;T;T;T;T;T;T;T;T;T;T;T;T;T;T

MetaSVM

Benign

-1.0

MutationAssessor

Benign

0.0

.;.;N;N;.;.;N;N;.;.;.;.;N;N;N

PrimateAI

Benign

0.40

PROVEAN

Benign

0.030

N;N;N;N;N;N;N;N;N;N;N;N;N;N;N

REVEL

Benign

0.052

Sift

Benign

0.30

T;T;T;T;T;T;T;T;T;T;T;T;T;T;T

Sift4G

Benign

0.60

T;T;T;T;T;T;T;T;T;T;T;T;T;T;T

Polyphen

0.96

D;.;B;B;.;.;B;.;.;.;.;.;.;B;B

Vest4

0.44

MutPred

0.22

.;.;Loss of glycosylation at P125 (P = 0.0135);Loss of glycosylation at P125 (P = 0.0135);Loss of glycosylation at P125 (P = 0.0135);Loss of glycosylation at P125 (P = 0.0135);Loss of glycosylation at P125 (P = 0.0135);Loss of glycosylation at P125 (P = 0.0135);.;.;.;.;Loss of glycosylation at P125 (P = 0.0135);Loss of glycosylation at P125 (P = 0.0135);Loss of glycosylation at P125 (P = 0.0135);

MVP

0.47

MPC

0.25

ClinPred

0.26

GERP RS

4.7

Varity_R

0.031

gMVP

0.61

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.11

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over