chr5-54583746-T-A

Position:

• chr5-54583746-T-A

Variant summary

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

The XM_017008997.2(SNX18):​c.1622-22657T>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 XM_017008997.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.19

Genes affected

SNX18 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SNX18	XM_017008997.2	c.1622-22657T>A		intron_variant
SNX18	XR_001741987.2	n.1816-22657T>A		intron_variant, non_coding_transcript_variant
SNX18	XR_007058577.1	n.1816-22657T>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.680

Gnomad4 AMR AF: 0.436

Gnomad4 ASJ AF: 0.407

Gnomad4 EAS AF: 0.335

Gnomad4 SAS AF: 0.574

Gnomad4 FIN AF: 0.332

Gnomad4 NFE AF: 0.397

Gnomad4 OTH AF: 0.485

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.019
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

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