rs2548621

Variant names:

• chr5-54606509-G-A
• rs2548621
• XM_017008997.2:c.*102G>A

Your query was ambiguous. Multiple possible variants found:

• chr5-54606509-G-A
• chr5-54606509-G-C
• chr5-54606509-G-T

Variant summary

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

The ENST00000799034.1(ENSG00000304037):​n.106+3G>A variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.896 in 152,120 control chromosomes in the GnomAD database, including 62,168 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 0.90 (62168 hom., cov: 31)
• Consequence: ENSG00000304037 ENST00000799034.1 splice_region, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.853
• Publications: 5 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]

ENSG00000304037 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.969 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000799034.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000304037	ENST00000799035.1		n.108G>A		non_coding_transcript_exon	Exon 1 of 3
	ENSG00000304037	ENST00000799034.1		n.106+3G>A		splice_region intron	N/A

Frequencies

GnomAD3 genomes AF: 0.896 AC: 136241 AN: 152002 Hom.: 62151 Cov.: 31

Gnomad AFR AF: 0.704

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.951

Gnomad ASJ AF: 0.967

Gnomad EAS AF: 0.909

Gnomad SAS AF: 0.980

Gnomad FIN AF: 0.976

Gnomad MID AF: 0.943

Gnomad NFE AF: 0.976

Gnomad OTH AF: 0.917

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

GnomAD4 genome AF: 0.896 AC: 136305 AN: 152120 Hom.: 62168 Cov.: 31 AF XY: 0.899 AC XY: 66864 AN XY: 74374

African (AFR) AF: 0.704 AC: 29136 AN: 41414

American (AMR) AF: 0.951 AC: 14536 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.967 AC: 3357 AN: 3470

East Asian (EAS) AF: 0.909 AC: 4697 AN: 5166

South Asian (SAS) AF: 0.980 AC: 4723 AN: 4820

European-Finnish (FIN) AF: 0.976 AC: 10361 AN: 10618

Middle Eastern (MID) AF: 0.942 AC: 277 AN: 294

European-Non Finnish (NFE) AF: 0.976 AC: 66363 AN: 68028

Other (OTH) AF: 0.918 AC: 1943 AN: 2116

Alfa AF: 0.949 Hom.: 225628

Bravo AF: 0.884

Asia WGS AF: 0.947 AC: 3296 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.20
DANN	Benign	0.72
PhyloP100		-0.85

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2548621;

hg19: chr5-53902339;