rs154499

Positions:

• chr5-122883971-A-C
• chr5-122883971-A-T

Variant summary

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

The NM_014035.4(SNX24):​c.60+38278A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.805 in 152,178 control chromosomes in the GnomAD database, including 50,106 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 0.81 (50106 hom., cov: 32)
• Consequence: SNX24 NM_014035.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.80

Genes affected

SNX24 (HGNC:21533): (sorting nexin 24) Predicted to enable phosphatidylinositol phosphate binding activity. Predicted to be involved in protein transport. Predicted to be located in cytoplasmic vesicle membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.965 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SNX24	NM_014035.4	c.60+38278A>C		intron_variant		ENST00000261369.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SNX24	ENST00000261369.9	c.60+38278A>C		intron_variant		1	NM_014035.4	P1

Frequencies

GnomAD3 genomes AF: 0.805 AC: 122419 AN: 152062 Hom.: 50053 Cov.: 32

Gnomad AFR AF: 0.929

Gnomad AMI AF: 0.771

Gnomad AMR AF: 0.824

Gnomad ASJ AF: 0.752

Gnomad EAS AF: 0.987

Gnomad SAS AF: 0.859

Gnomad FIN AF: 0.791

Gnomad MID AF: 0.759

Gnomad NFE AF: 0.713

Gnomad OTH AF: 0.801

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

GnomAD4 genome AF: 0.805 AC: 122533 AN: 152178 Hom.: 50106 Cov.: 32 AF XY: 0.811 AC XY: 60328 AN XY: 74398

Gnomad4 AFR AF: 0.929

Gnomad4 AMR AF: 0.824

Gnomad4 ASJ AF: 0.752

Gnomad4 EAS AF: 0.987

Gnomad4 SAS AF: 0.858

Gnomad4 FIN AF: 0.791

Gnomad4 NFE AF: 0.713

Gnomad4 OTH AF: 0.804

Alfa AF: 0.667 Hom.: 1919

Bravo AF: 0.813

Asia WGS AF: 0.928 AC: 3224 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.028
DANN	Benign	0.38

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs154499; hg19: chr5-122219666; COSMIC: COSV54448023;