5-122932309-C-T

Variant names:

• chr5-122932309-C-T
• rs6595416
• NM_014035.4:c.61-4425C>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.61-4425C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.362 in 151,914 control chromosomes in the GnomAD database, including 10,692 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 0.36 (10692 hom., cov: 32)
• Consequence: SNX24 NM_014035.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0800
• Publications: 5 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=-0.75).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.472 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SNX24	NM_014035.4	c.61-4425C>T		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.61-4425C>T		intron_variant	Intron 1 of 6	1	NM_014035.4	ENSP00000261369.4

Frequencies

GnomAD3 genomes AF: 0.362 AC: 54918 AN: 151798 Hom.: 10682 Cov.: 32

Gnomad AFR AF: 0.478

Gnomad AMI AF: 0.349

Gnomad AMR AF: 0.381

Gnomad ASJ AF: 0.289

Gnomad EAS AF: 0.0491

Gnomad SAS AF: 0.149

Gnomad FIN AF: 0.329

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.335

Gnomad OTH AF: 0.372

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

GnomAD4 genome AF: 0.362 AC: 54957 AN: 151914 Hom.: 10692 Cov.: 32 AF XY: 0.355 AC XY: 26324 AN XY: 74250

African (AFR) AF: 0.478 AC: 19775 AN: 41408

American (AMR) AF: 0.381 AC: 5815 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.289 AC: 1003 AN: 3466

East Asian (EAS) AF: 0.0490 AC: 254 AN: 5186

South Asian (SAS) AF: 0.149 AC: 718 AN: 4824

European-Finnish (FIN) AF: 0.329 AC: 3457 AN: 10500

Middle Eastern (MID) AF: 0.303 AC: 89 AN: 294

European-Non Finnish (NFE) AF: 0.335 AC: 22748 AN: 67950

Other (OTH) AF: 0.369 AC: 780 AN: 2112

Alfa AF: 0.267 Hom.: 972

Bravo AF: 0.374

Asia WGS AF: 0.135 AC: 470 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	12
DANN	Benign	0.84
PhyloP100		-0.080
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: rs6595416; hg19: chr5-122268004;