rs1313810182

Variant names:

• chr5-134905155-G-C
• rs1313810182
• NM_032151.5:c.16G>C

Your query was ambiguous. Multiple possible variants found:

• chr5-134905155-G-C
• chr5-134905155-G-T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_032151.5(PCBD2):​c.16G>C​(p.Gly6Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000841 in 1,069,732 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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G6W) has been classified as Likely benign.

• Frequency:
  • Genomes: not found (cov: 33)
  • Exomes 𝑓: 0.0000084 (0 hom.)
• Consequence: PCBD2 NM_032151.5 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.37

Genes affected

PCBD2 (HGNC:24474): (pterin-4 alpha-carbinolamine dehydratase 2) Predicted to enable 4-alpha-hydroxytetrahydrobiopterin dehydratase activity. Involved in positive regulation of transcription, DNA-templated. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000279799 (HGNC:):

ACMG classification

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=0.15355092).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PCBD2	NM_032151.5	c.16G>C	p.Gly6Arg	missense_variant	Exon 1 of 4	ENST00000254908.11	NP_115527.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PCBD2	ENST00000254908.11	c.16G>C	p.Gly6Arg	missense_variant	Exon 1 of 4	1	NM_032151.5	ENSP00000254908.6
PCBD2	ENST00000512783.5	c.16G>C	p.Gly6Arg	missense_variant	Exon 1 of 5	1		ENSP00000421544.1
PCBD2	ENST00000504352.1	n.-18G>C		upstream_gene_variant		5		ENSP00000426161.1
ENSG00000279799	ENST00000623591.1	n.-80G>C		upstream_gene_variant		6

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome AF: 0.00000841 AC: 9 AN: 1069732 Hom.: 0 Cov.: 31 AF XY: 0.00000989 AC XY: 5 AN XY: 505562

Gnomad4 AFR exome AF: 0.0000445

Gnomad4 AMR exome AF: 0.00

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: 0.00000766

Gnomad4 OTH exome AF: 0.0000234

GnomAD4 genome Cov.: 33

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.32
BayesDel_addAF	Benign	-0.014	T
BayesDel_noAF	Benign	-0.26
CADD	Benign	0.77
DANN	Benign	0.78
DEOGEN2	Benign	0.016	T;T
Eigen	Benign	-1.9
Eigen_PC	Benign	-2.0
FATHMM_MKL	Benign	0.016	N
LIST_S2	Benign	0.47	.;T
M_CAP	Pathogenic	0.89	D
MetaRNN	Benign	0.15	T;T
MetaSVM	Benign	-0.67	T
MutationAssessor	Benign	1.1	L;L
PrimateAI	Uncertain	0.76	T
PROVEAN	Benign	-0.16	N;N
REVEL	Benign	0.18
Sift	Benign	0.31	T;T
Sift4G	Benign	0.25	T;T
Polyphen		0.0	B;B
Vest4		0.14
MutPred		0.34		Gain of MoRF binding (P = 0.0028);Gain of MoRF binding (P = 0.0028);
MVP		0.57
MPC		0.25
ClinPred		0.12	T
GERP RS		-5.2
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.3
Varity_R		0.062
gMVP		0.59

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: rs1313810182; hg19: chr5-134240845;