16-50675812-G-T

Variant names:

• chr16-50675812-G-T
• rs6596
• NM_182854.4:c.240C>A

Variant summary

Our verdict is Likely benign. The variant received -3 ACMG points: 2P and 5B. PM2 BP4_Strong BP7

The NM_182854.4(SNX20):​c.240C>A​(p.Ile80Ile) variant causes a synonymous 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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: SNX20 NM_182854.4 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0280
• Publications: 0 publications found

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

Our verdict: Likely_benign. The variant received -3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.49).
• BP7: Synonymous conserved (PhyloP=-0.028 with no splicing effect.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_182854.4. 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
	SNX20	NM_182854.4	MANE Select	c.240C>A	p.Ile80Ile	synonymous	Exon 3 of 4	NP_878274.1	Q7Z614-1
	SNX20	NM_153337.3		c.240C>A	p.Ile80Ile	synonymous	Exon 3 of 4	NP_699168.1	Q7Z614-3
	SNX20	NM_001144972.2		c.240C>A	p.Ile80Ile	synonymous	Exon 3 of 4	NP_001138444.1	Q7Z614-4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SNX20	ENST00000330943.9	TSL:1 MANE Select	c.240C>A	p.Ile80Ile	synonymous	Exon 3 of 4	ENSP00000332062.4	Q7Z614-1
	SNX20	ENST00000423026.6	TSL:1	c.240C>A	p.Ile80Ile	synonymous	Exon 3 of 4	ENSP00000388875.2	Q7Z614-4
	SNX20	ENST00000568993.5	TSL:1	n.240C>A		non_coding_transcript_exon	Exon 3 of 5	ENSP00000454863.1	Q7Z614-3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.49
CADD	Benign	2.9
DANN	Benign	0.79
PhyloP100		-0.028

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

Other links and lift over

dbSNP: rs6596; hg19: chr16-50709723;