X-16719832-G-T

Position:

• chrX-16719832-G-T

Variant summary

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

The NM_032796.4(SYAP1):​c.108G>T​(p.Glu36Asp) 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. 12/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 24)
• Consequence: SYAP1 NM_032796.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.02

Genes affected

SYAP1 (HGNC:16273): (synapse associated protein 1) Involved in several processes, including TORC2 signaling; cellular response to growth factor stimulus; and cellular response to peptide hormone stimulus. Located in Golgi apparatus; cytosol; and nucleoplasm. Is extrinsic component of cytoplasmic side of plasma membrane. [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=0.1258637).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SYAP1	NM_032796.4	c.108G>T	p.Glu36Asp	missense_variant	1/9	ENST00000380155.4
SYAP1	NR_033181.2	n.221G>T		non_coding_transcript_exon_variant	1/9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SYAP1	ENST00000380155.4	c.108G>T	p.Glu36Asp	missense_variant	1/9	1	NM_032796.4	P1
SYAP1	ENST00000495743.1	n.62G>T		non_coding_transcript_exon_variant	1/3	2

Frequencies

GnomAD3 genomes Cov.: 24

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 24

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.081
BayesDel_addAF	Benign	-0.37	T
BayesDel_noAF	Benign	-0.78
CADD	Benign	13
DANN	Benign	0.75
DEOGEN2	Benign	0.12	T
FATHMM_MKL	Benign	0.71	D
LIST_S2	Benign	0.45	T
M_CAP	Uncertain	0.12	D
MetaRNN	Benign	0.13	T
MetaSVM	Benign	-0.96	T
MutationAssessor	Uncertain	2.3	M
MutationTaster	Benign	1.0	N
PrimateAI	Benign	0.42	T
PROVEAN	Benign	-0.10	N
REVEL	Benign	0.078
Sift	Benign	0.16	T
Sift4G	Benign	0.41	T
Polyphen		0.039	B
Vest4		0.12
MutPred		0.11		Gain of glycosylation at S37 (P = 0.1484);
MVP		0.38
MPC		0.47
ClinPred		0.37	T
GERP RS		5.1
Varity_R		0.091
gMVP		0.32

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: chrX-16737955;