WSCD2 p.Lys123Asn

Variant names:

• chr12-108196201-G-T
• NM_014653.4:c.369G>T
• WSCD2 p.Lys123Asn

Your query was ambiguous. Multiple possible variants found:

• chr12-108196201-G-T
• chr12-108196201-G-C

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_014653.4(WSCD2):​c.369G>T​(p.Lys123Asn) 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 benign outcome for this variant. 14/22 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 nucleotide change resulting in the same amino acid substitution has been previously reported as Uncertain significance in ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: WSCD2 NM_014653.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.76
• Publications: 0 publications found

Genes affected

WSCD2 (HGNC:29117): (WSC domain containing 2) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000307044 (HGNC:):

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.08791256).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014653.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	WSCD2	NM_014653.4	MANE Select	c.369G>T	p.Lys123Asn	missense	Exon 2 of 9	NP_055468.2
	WSCD2	NM_001304447.2		c.369G>T	p.Lys123Asn	missense	Exon 3 of 10	NP_001291376.1	Q2TBF2-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	WSCD2	ENST00000547525.6	TSL:1 MANE Select	c.369G>T	p.Lys123Asn	missense	Exon 2 of 9	ENSP00000448047.1	Q2TBF2-1
	WSCD2	ENST00000332082.8	TSL:1	c.369G>T	p.Lys123Asn	missense	Exon 3 of 10	ENSP00000331933.4	Q2TBF2-1
	WSCD2	ENST00000549903.1	TSL:5	c.369G>T	p.Lys123Asn	missense	Exon 1 of 9	ENSP00000447272.1	Q2TBF2-2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.30
BayesDel_addAF	Benign	-0.25	T
BayesDel_noAF	Benign	-0.60
CADD	Benign	19
DANN	Uncertain	0.98
DEOGEN2	Benign	0.011	T
Eigen	Benign	-0.23
Eigen_PC	Benign	-0.13
FATHMM_MKL	Uncertain	0.97	D
LIST_S2	Benign	0.78	T
M_CAP	Benign	0.0070	T
MetaRNN	Benign	0.088	T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	1.8	L
PhyloP100		1.8
PrimateAI	Uncertain	0.67	T
PROVEAN	Benign	-1.4	N
REVEL	Benign	0.016
Sift	Benign	0.43	T
Sift4G	Benign	0.38	T
PromoterAI		0.014	Neutral
Varity_R		0.086
gMVP		0.85
Mutation Taster		=91/9	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

hg19: chr12-108589978;