16-50675812-G-T

Variant names:

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

Variant summary

Our verdict is Likely benign. Variant got -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

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 Likely_benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SNX20	NM_182854.4	c.240C>A	p.Ile80Ile	synonymous_variant	Exon 3 of 4	ENST00000330943.9	NP_878274.1
SNX20	NM_153337.3	c.240C>A	p.Ile80Ile	synonymous_variant	Exon 3 of 4		NP_699168.1
SNX20	NM_001144972.2	c.240C>A	p.Ile80Ile	synonymous_variant	Exon 3 of 4		NP_001138444.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SNX20	ENST00000330943.9	c.240C>A	p.Ile80Ile	synonymous_variant	Exon 3 of 4	1	NM_182854.4	ENSP00000332062.4
SNX20	ENST00000423026.6	c.240C>A	p.Ile80Ile	synonymous_variant	Exon 3 of 4	1		ENSP00000388875.2
SNX20	ENST00000568993.5	n.240C>A		non_coding_transcript_exon_variant	Exon 3 of 5	1		ENSP00000454863.1
SNX20	ENST00000300590.7	c.240C>A	p.Ile80Ile	synonymous_variant	Exon 3 of 4	2		ENSP00000300590.3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr16-50709723;