5-54580152-T-C

Variant names:

• chr5-54580152-T-C
• rs1122401
• XM_017008997.2:c.1622-26251T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_001741987.2(SNX18):​n.1816-26251T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.308 in 151,724 control chromosomes in the GnomAD database, including 7,528 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 0.31 (7528 hom., cov: 32)
• Consequence: SNX18 XR_001741987.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.635
• Publications: 4 publications found

Genes affected

SNX18 (HGNC:19245): (sorting nexin 18) This gene encodes a member of the sorting nexin family. Members of this family contain a phox (PX) domain, which is a phosphoinositide binding domain, and are involved in intracellular trafficking. This protein does not contain a coiled coil region, like some family members, but contains a SH3 domain. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.385 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.308 AC: 46724 AN: 151606 Hom.: 7507 Cov.: 32

Gnomad AFR AF: 0.390

Gnomad AMI AF: 0.153

Gnomad AMR AF: 0.289

Gnomad ASJ AF: 0.335

Gnomad EAS AF: 0.392

Gnomad SAS AF: 0.330

Gnomad FIN AF: 0.252

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.265

Gnomad OTH AF: 0.310

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.308 AC: 46801 AN: 151724 Hom.: 7528 Cov.: 32 AF XY: 0.308 AC XY: 22839 AN XY: 74152

African (AFR) AF: 0.390 AC: 16126 AN: 41308

American (AMR) AF: 0.289 AC: 4403 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.335 AC: 1161 AN: 3470

East Asian (EAS) AF: 0.392 AC: 2014 AN: 5142

South Asian (SAS) AF: 0.330 AC: 1587 AN: 4802

European-Finnish (FIN) AF: 0.252 AC: 2655 AN: 10532

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.265 AC: 17977 AN: 67912

Other (OTH) AF: 0.315 AC: 666 AN: 2112

Alfa AF: 0.290 Hom.: 11740

Bravo AF: 0.316

Asia WGS AF: 0.381 AC: 1325 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.73
DANN	Benign	0.35
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs1122401; hg19: chr5-53875982;