chr5-122883971-A-C

Variant names:

• chr5-122883971-A-C
• rs154499
• NM_014035.4:c.60+38278A>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
SNX24	NM_014035.4	c.60+38278A>C		intron_variant	Intron 1 of 6	ENST00000261369.9	NP_054754.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SNX24	ENST00000261369.9	c.60+38278A>C		intron_variant	Intron 1 of 6	1	NM_014035.4	ENSP00000261369.4

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

African (AFR) AF: 0.929 AC: 38599 AN: 41536

American (AMR) AF: 0.824 AC: 12598 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.752 AC: 2611 AN: 3472

East Asian (EAS) AF: 0.987 AC: 5111 AN: 5176

South Asian (SAS) AF: 0.858 AC: 4142 AN: 4826

European-Finnish (FIN) AF: 0.791 AC: 8366 AN: 10578

Middle Eastern (MID) AF: 0.762 AC: 224 AN: 294

European-Non Finnish (NFE) AF: 0.713 AC: 48483 AN: 67990

Other (OTH) AF: 0.804 AC: 1697 AN: 2112

Alfa AF: 0.690 Hom.: 2245

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
PhyloP100		-4.8
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

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