rs2447820

chr5-122929041-G-T

Variant summary

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

The NM_014035.4(SNX24):c.61-7693G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.17 in 151,802 control chromosomes in the GnomAD database, including 2,717 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 0.17 (2717 hom., cov: 30)
• Consequence: SNX24 NM_014035.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0140

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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.457 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SNX24	NM_014035.4	c.61-7693G>T		intron_variant		ENST00000261369.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SNX24	ENST00000261369.9	c.61-7693G>T		intron_variant		1	NM_014035.4	P1

Frequencies

GnomAD3 genomes AF: 0.170 AC: 25745 AN: 151682 Hom.: 2702 Cov.: 30

Gnomad AFR AF: 0.168

Gnomad AMI AF: 0.221

Gnomad AMR AF: 0.230

Gnomad ASJ AF: 0.202

Gnomad EAS AF: 0.472

Gnomad SAS AF: 0.364

Gnomad FIN AF: 0.145

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.122

Gnomad OTH AF: 0.181

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

GnomAD4 genome AF: 0.170 AC: 25784 AN: 151802 Hom.: 2717 Cov.: 30 AF XY: 0.178 AC XY: 13187 AN XY: 74214

Gnomad4 AFR AF: 0.168

Gnomad4 AMR AF: 0.230

Gnomad4 ASJ AF: 0.202

Gnomad4 EAS AF: 0.472

Gnomad4 SAS AF: 0.364

Gnomad4 FIN AF: 0.145

Gnomad4 NFE AF: 0.122

Gnomad4 OTH AF: 0.185

Alfa AF: 0.147 Hom.: 1146

Bravo AF: 0.177

Asia WGS AF: 0.370 AC: 1284 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	1.9
Dann	Benign	0.70

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: rs2447820; hg19: chr5-122264736;