rs55829948

Variant names:

• chr22-50551313-C-A
• NM_001123225.3:c.199G>T

Your query was ambiguous. Multiple possible variants found:

• chr22-50551313-C-A
• chr22-50551313-C-G
• chr22-50551313-C-T

Variant summary

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

The NM_001123225.3(SYCE3):​c.199G>T​(p.Val67Phe) 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. 14/19 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. V67I) has been classified as Benign.

• Frequency: Genomes: not found (cov: 33)
• Consequence: SYCE3 NM_001123225.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.47

Genes affected

SYCE3 (HGNC:35245): (synaptonemal complex central element protein 3) Predicted to be involved in reciprocal meiotic recombination; spermatogenesis; and synaptonemal complex assembly. Predicted to act upstream of or within positive regulation of apoptotic process. Predicted to be located in chromosome and nucleus. Predicted to be active in central element. [provided by Alliance of Genome Resources, Apr 2022]

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=0.08970812).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SYCE3	NM_001123225.3	c.199G>T	p.Val67Phe	missense_variant	Exon 3 of 3	ENST00000406915.4	NP_001116697.1
SYCE3	XM_024452261.2	c.199G>T	p.Val67Phe	missense_variant	Exon 3 of 3		XP_024308029.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SYCE3	ENST00000406915.4	c.199G>T	p.Val67Phe	missense_variant	Exon 3 of 3	2	NM_001123225.3	ENSP00000385480.3
SYCE3	ENST00000402753.1	c.199G>T	p.Val67Phe	missense_variant	Exon 2 of 2	1		ENSP00000385122.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.10
BayesDel_addAF	Benign	-0.22	T
BayesDel_noAF	Benign	-0.55
CADD	Benign	21
DANN	Benign	0.94
DEOGEN2	Benign	0.084	T;T
Eigen	Benign	-0.40
Eigen_PC	Benign	-0.25
FATHMM_MKL	Benign	0.54	D
LIST_S2	Benign	0.57	.;T
M_CAP	Benign	0.0054	T
MetaRNN	Benign	0.090	T;T
MetaSVM	Benign	-1.0	T
PrimateAI	Benign	0.33	T
PROVEAN	Benign	-0.34	N;N
REVEL	Benign	0.047
Sift	Benign	0.21	T;T
Sift4G	Benign	0.28	T;T
Polyphen		0.0	B;B
Vest4		0.17
MutPred		0.19		Loss of ubiquitination at K70 (P = 0.1664);Loss of ubiquitination at K70 (P = 0.1664);
MVP		0.33
ClinPred		0.14	T
GERP RS		2.4
Varity_R		0.076
gMVP		0.71

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: chr22-50989742;