rs246295

chr5-122912254-C-T

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The NM_014035.4(SNX24):c.61-24480C>T variant causes a intron change. 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 (8577 hom., cov: 17)
  • Failed GnomAD Quality Control
• Consequence: SNX24 NM_014035.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: No conservation score assigned

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 Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SNX24	NM_014035.4	c.61-24480C>T		intron_variant		ENST00000261369.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SNX24	ENST00000261369.9	c.61-24480C>T		intron_variant		1	NM_014035.4	P1

Frequencies

GnomAD3 genomes AF: 0.00 AC: 44574 AN: 124860 Hom.: 8561 Cov.: 17 FAILED QC

Gnomad AFR AF: 0.380

Gnomad AMI AF: 0.283

Gnomad AMR AF: 0.360

Gnomad ASJ AF: 0.345

Gnomad EAS AF: 0.901

Gnomad SAS AF: 0.596

Gnomad FIN AF: 0.374

Gnomad MID AF: 0.365

Gnomad NFE AF: 0.299

Gnomad OTH AF: 0.348

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

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.357 AC: 44618 AN: 124934 Hom.: 8577 Cov.: 17 AF XY: 0.364 AC XY: 21517 AN XY: 59054

Gnomad4 AFR AF: 0.380

Gnomad4 AMR AF: 0.360

Gnomad4 ASJ AF: 0.345

Gnomad4 EAS AF: 0.901

Gnomad4 SAS AF: 0.594

Gnomad4 FIN AF: 0.374

Gnomad4 NFE AF: 0.299

Gnomad4 OTH AF: 0.354

Alfa AF: 0.374 Hom.: 1166

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	1.2
Dann	Benign	0.82

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: rs246295; hg19: chr5-122247949;