5-122929041-G-T

Variant names:

• chr5-122929041-G-T
• rs2447820
• NM_014035.4:c.61-7693G>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 9 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.457 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SNX24	NM_014035.4	MANE Select	c.61-7693G>T		intron	N/A	NP_054754.1
	SNX24	NR_146145.2		n.82-7693G>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SNX24	ENST00000261369.9	TSL:1 MANE Select	c.61-7693G>T		intron	N/A	ENSP00000261369.4
	SNX24	ENST00000506996.5	TSL:1	c.61-7693G>T		intron	N/A	ENSP00000422535.1
	SNX24	ENST00000513881.5	TSL:1	c.61-7693G>T		intron	N/A	ENSP00000424149.1

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

African (AFR) AF: 0.168 AC: 6959 AN: 41456

American (AMR) AF: 0.230 AC: 3505 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.202 AC: 700 AN: 3472

East Asian (EAS) AF: 0.472 AC: 2381 AN: 5040

South Asian (SAS) AF: 0.364 AC: 1747 AN: 4796

European-Finnish (FIN) AF: 0.145 AC: 1528 AN: 10568

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.122 AC: 8316 AN: 67916

Other (OTH) AF: 0.185 AC: 388 AN: 2102

Alfa AF: 0.148 Hom.: 1308

Bravo AF: 0.177

Asia WGS AF: 0.370 AC: 1284 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.9
DANN	Benign	0.70
PhyloP100		0.014
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: rs2447820; hg19: chr5-122264736;