chr16-50670251-T-C

Position:

• chr16-50670251-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000423026.6(SNX20):​c.283-2210A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0406 in 152,438 control chromosomes in the GnomAD database, including 321 homozygotes. 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: 𝑓 0.041 (321 hom., cov: 32)
  • Exomes 𝑓: 0.0050 (0 hom.)
• Consequence: SNX20 ENST00000423026.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.32

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.13 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC101927272	NR_110908.1	n.307-432T>C		intron_variant, non_coding_transcript_variant
SNX20	NM_001144972.2	c.283-2210A>G		intron_variant			NP_001138444.1
SNX20	NM_153337.3	c.283-1103A>G		intron_variant			NP_699168.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000570241.3	n.4259-432T>C		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.0406 AC: 6177 AN: 152118 Hom.: 322 Cov.: 32

Gnomad AFR AF: 0.114

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0311

Gnomad ASJ AF: 0.000576

Gnomad EAS AF: 0.139

Gnomad SAS AF: 0.00766

Gnomad FIN AF: 0.00782

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00113

Gnomad OTH AF: 0.0368

GnomAD4 exome AF: 0.00495 AC: 1 AN: 202 Hom.: 0 Cov.: 0 AF XY: 0.00610 AC XY: 1 AN XY: 164

Gnomad4 AFR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00602

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0407 AC: 6190 AN: 152236 Hom.: 321 Cov.: 32 AF XY: 0.0397 AC XY: 2956 AN XY: 74440

Gnomad4 AFR AF: 0.114

Gnomad4 AMR AF: 0.0310

Gnomad4 ASJ AF: 0.000576

Gnomad4 EAS AF: 0.139

Gnomad4 SAS AF: 0.00746

Gnomad4 FIN AF: 0.00782

Gnomad4 NFE AF: 0.00113

Gnomad4 OTH AF: 0.0364

Alfa AF: 0.0274 Hom.: 27

Bravo AF: 0.0481

Asia WGS AF: 0.0650 AC: 227 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.29
DANN	Benign	0.35

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs8059649; hg19: chr16-50704162;