16-50677423-G-C

Variant names:

• chr16-50677423-G-C
• NM_182854.4:c.104C>G

Variant summary

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

The NM_182854.4(SNX20):​c.104C>G​(p.Pro35Arg) 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. 13/21 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. P35L) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 32)
• Consequence: SNX20 NM_182854.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0350

Genes affected

SNX20 (HGNC:30390): (sorting nexin 20) SNX20 interacts with the cytoplasmic domain of PSGL1 (SELPLG; MIM 600738) and cycles PSGL1 into endosomes.[supplied by OMIM, Feb 2010]

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=0.082711786).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SNX20	NM_182854.4	c.104C>G	p.Pro35Arg	missense_variant	Exon 2 of 4	ENST00000330943.9	NP_878274.1
SNX20	NM_153337.3	c.104C>G	p.Pro35Arg	missense_variant	Exon 2 of 4		NP_699168.1
SNX20	NM_001144972.2	c.104C>G	p.Pro35Arg	missense_variant	Exon 2 of 4		NP_001138444.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SNX20	ENST00000330943.9	c.104C>G	p.Pro35Arg	missense_variant	Exon 2 of 4	1	NM_182854.4	ENSP00000332062.4
SNX20	ENST00000423026.6	c.104C>G	p.Pro35Arg	missense_variant	Exon 2 of 4	1		ENSP00000388875.2
SNX20	ENST00000568993.5	n.104C>G		non_coding_transcript_exon_variant	Exon 2 of 5	1		ENSP00000454863.1
SNX20	ENST00000300590.7	c.104C>G	p.Pro35Arg	missense_variant	Exon 2 of 4	2		ENSP00000300590.3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.096
BayesDel_addAF	Benign	-0.21	T
BayesDel_noAF	Benign	-0.54
CADD	Benign	9.5
DANN	Benign	0.86
DEOGEN2	Benign	0.012	.;.;T;.
Eigen	Benign	-1.2
Eigen_PC	Benign	-1.4
FATHMM_MKL	Benign	0.10	N
LIST_S2	Benign	0.67	T;.;T;T
M_CAP	Benign	0.019	T
MetaRNN	Benign	0.083	T;T;T;T
MetaSVM	Benign	-0.92	T
MutationAssessor	Uncertain	2.3	M;M;M;.
PrimateAI	Benign	0.30	T
PROVEAN	Uncertain	-3.3	D;D;N;.
REVEL	Benign	0.075
Sift	Benign	0.064	T;T;T;.
Sift4G	Benign	0.54	T;T;T;T
Polyphen		0.83	P;P;P;.
Vest4		0.28
MutPred		0.19		Gain of solvent accessibility (P = 0.0055);Gain of solvent accessibility (P = 0.0055);Gain of solvent accessibility (P = 0.0055);Gain of solvent accessibility (P = 0.0055);
MVP		0.16
MPC		1.2
ClinPred		0.45	T
GERP RS		-0.37
Varity_R		0.043
gMVP		0.31

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: chr16-50711334;