5-138084562-T-G

Position:

• chr5-138084562-T-G

Variant summary

Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2 PP3

The NM_001300939.2(WNT8A):​c.221T>G​(p.Phe74Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: WNT8A NM_001300939.2 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 2.62

Genes affected

WNT8A (HGNC:12788): (Wnt family member 8A) The WNT gene family consists of structurally related genes which encode secreted signaling proteins. These proteins have been implicated in oncogenesis and in several developmental processes, including regulation of cell fate and patterning during embryogenesis. This gene is a member of the WNT gene family, and may be implicated in development of early embryos as well as germ cell tumors. Multiple alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Jul 2014]

ACMG classification

Verdict is Uncertain_significance. Variant got 3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.792

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
WNT8A	NM_001300939.2	c.221T>G	p.Phe74Cys	missense_variant	2/5	ENST00000506684.6	NP_001287868.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
WNT8A	ENST00000506684.6	c.221T>G	p.Phe74Cys	missense_variant	2/5	1	NM_001300939.2	ENSP00000426653.1
WNT8A	ENST00000504809.5	c.221T>G	p.Phe74Cys	missense_variant	2/6	1		ENSP00000424809.1
WNT8A	ENST00000398754.1	c.167T>G	p.Phe56Cys	missense_variant	3/6	1		ENSP00000381739.1
WNT8A	ENST00000361560.6	n.167T>G		non_coding_transcript_exon_variant	3/8	1		ENSP00000354726.2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 32

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Sep 27, 2024

The c.167T>G (p.F56C) alteration is located in exon 3 (coding exon 3) of the WNT8A gene. This alteration results from a T to G substitution at nucleotide position 167, causing the phenylalanine (F) at amino acid position 56 to be replaced by a cysteine (C). 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	Uncertain	0.52
BayesDel_addAF	Pathogenic	0.16	D
BayesDel_noAF	Uncertain	0.0
CADD	Pathogenic	28
DANN	Uncertain	0.99
DEOGEN2	Pathogenic	0.87	.;.;D
Eigen	Uncertain	0.60
Eigen_PC	Uncertain	0.56
FATHMM_MKL	Uncertain	0.91	D
LIST_S2	Uncertain	0.88	D;D;D
M_CAP	Uncertain	0.12	D
MetaRNN	Pathogenic	0.79	D;D;D
MetaSVM	Uncertain	0.14	D
MutationAssessor	Uncertain	2.5	.;.;M
PrimateAI	Uncertain	0.77	T
PROVEAN	Uncertain	-3.5	D;D;D
REVEL	Pathogenic	0.70
Sift	Uncertain	0.013	D;D;D
Sift4G	Uncertain	0.047	D;T;D
Polyphen		1.0	D;D;D
Vest4		0.64
MutPred		0.60		Loss of ubiquitination at K73 (P = 0.0982);Loss of ubiquitination at K73 (P = 0.0982);.;
MVP		0.56
MPC		1.1
ClinPred		0.99	D
GERP RS		5.0
Varity_R		0.44
gMVP		0.73

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr5-137420251;