ENST00000799035.1:n.108G>A

Variant names:

• chr5-54606509-G-A
• rs2548621
• ENST00000799035.1:n.108G>A

Variant summary

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

The ENST00000799035.1(ENSG00000304037):​n.108G>A variant causes a non coding transcript exon 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 ENST00000799035.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.853
• Publications: 5 publications found

Genes affected

ENSG00000304037 (HGNC:):

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=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.969 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SNX18	XM_017008997.2	c.*102G>A		3_prime_UTR_variant	Exon 2 of 2		XP_016864486.1
SNX18	XR_001741987.2	n.1919+3G>A		splice_region_variant, intron_variant	Intron 2 of 2
SNX18	XR_007058577.1	n.1919+3G>A		splice_region_variant, intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000304037	ENST00000799035.1	n.108G>A		non_coding_transcript_exon_variant	Exon 1 of 3
ENSG00000304037	ENST00000799034.1	n.106+3G>A		splice_region_variant, intron_variant	Intron 1 of 2

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 v4.3

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

Other links and lift over

dbSNP: rs2548621; hg19: chr5-53902339;