chr5-122958007-A-G

Variant names:

• chr5-122958007-A-G
• rs30066
• NM_014035.4:c.249+11848A>G

Variant summary

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

The NM_014035.4(SNX24):​c.249+11848A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.806 in 152,114 control chromosomes in the GnomAD database, including 50,175 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 (50175 hom., cov: 31)
• Consequence: SNX24 NM_014035.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.49
• Publications: 12 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=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.965 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014035.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SNX24	NM_014035.4	MANE Select	c.249+11848A>G		intron	N/A	NP_054754.1	Q9Y343-1
	SNX24	NR_146145.2		n.270+11848A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SNX24	ENST00000261369.9	TSL:1 MANE Select	c.249+11848A>G		intron	N/A	ENSP00000261369.4	Q9Y343-1
	SNX24	ENST00000506996.5	TSL:1	c.249+11848A>G		intron	N/A	ENSP00000422535.1	Q9Y343-2
	SNX24	ENST00000513881.5	TSL:1	c.249+11848A>G		intron	N/A	ENSP00000424149.1	Q9Y343-2

Frequencies

GnomAD3 genomes AF: 0.806 AC: 122470 AN: 151996 Hom.: 50120 Cov.: 31

Gnomad AFR AF: 0.930

Gnomad AMI AF: 0.773

Gnomad AMR AF: 0.825

Gnomad ASJ AF: 0.755

Gnomad EAS AF: 0.987

Gnomad SAS AF: 0.861

Gnomad FIN AF: 0.791

Gnomad MID AF: 0.759

Gnomad NFE AF: 0.714

Gnomad OTH AF: 0.801

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

GnomAD4 genome AF: 0.806 AC: 122587 AN: 152114 Hom.: 50175 Cov.: 31 AF XY: 0.812 AC XY: 60347 AN XY: 74358

African (AFR) AF: 0.930 AC: 38635 AN: 41532

American (AMR) AF: 0.825 AC: 12613 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.755 AC: 2620 AN: 3470

East Asian (EAS) AF: 0.987 AC: 5112 AN: 5178

South Asian (SAS) AF: 0.859 AC: 4134 AN: 4810

European-Finnish (FIN) AF: 0.791 AC: 8348 AN: 10552

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

European-Non Finnish (NFE) AF: 0.714 AC: 48499 AN: 67964

Other (OTH) AF: 0.803 AC: 1699 AN: 2116

Alfa AF: 0.763 Hom.: 5506

Bravo AF: 0.814

Asia WGS AF: 0.928 AC: 3218 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.72
DANN	Benign	0.61
PhyloP100		-1.5
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: rs30066; hg19: chr5-122293702; COSMIC: COSV54449166;