rs714459

Variant names:

• chr5-54583746-T-A
• rs714459
• XM_017008997.2:c.1622-22657T>A

Variant summary

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

The XR_001741987.2(SNX18):​n.1816-22657T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.479 in 152,112 control chromosomes in the GnomAD database, including 18,738 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 0.48 (18738 hom., cov: 33)
• Consequence: SNX18 XR_001741987.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.19
• Publications: 0 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 (AFR) allele frequency at 95% confidence interval = 0.673 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: 0.479 AC: 72783 AN: 151994 Hom.: 18712 Cov.: 33

Gnomad AFR AF: 0.680

Gnomad AMI AF: 0.465

Gnomad AMR AF: 0.436

Gnomad ASJ AF: 0.407

Gnomad EAS AF: 0.334

Gnomad SAS AF: 0.575

Gnomad FIN AF: 0.332

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.397

Gnomad OTH AF: 0.479

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

GnomAD4 genome AF: 0.479 AC: 72861 AN: 152112 Hom.: 18738 Cov.: 33 AF XY: 0.476 AC XY: 35435 AN XY: 74372

African (AFR) AF: 0.680 AC: 28209 AN: 41494

American (AMR) AF: 0.436 AC: 6665 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.407 AC: 1413 AN: 3470

East Asian (EAS) AF: 0.335 AC: 1735 AN: 5178

South Asian (SAS) AF: 0.574 AC: 2772 AN: 4826

European-Finnish (FIN) AF: 0.332 AC: 3507 AN: 10566

Middle Eastern (MID) AF: 0.459 AC: 135 AN: 294

European-Non Finnish (NFE) AF: 0.397 AC: 26978 AN: 67964

Other (OTH) AF: 0.485 AC: 1024 AN: 2112

Alfa AF: 0.439 Hom.: 2178

Bravo AF: 0.491

Asia WGS AF: 0.506 AC: 1760 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	0.019
DANN	Benign	0.50
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs714459; hg19: chr5-53879576; COSMIC: COSV60132615;