rs2310160

Variant names:

• chr4-185269140-C-T
• rs2310160
• NM_001378034.2:c.1091+1985C>T

Variant summary

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

The NM_001378034.2(SNX25):​c.1091+1985C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.424 in 151,842 control chromosomes in the GnomAD database, including 13,831 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 0.42 (13831 hom., cov: 31)
• Consequence: SNX25 NM_001378034.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02
• Publications: 7 publications found

Genes affected

SNX25 (HGNC:21883): (sorting nexin 25) Predicted to enable type I transforming growth factor beta receptor binding activity. Involved in negative regulation of pathway-restricted SMAD protein phosphorylation; negative regulation of transforming growth factor beta receptor signaling pathway; and receptor catabolic process. Located in intracellular membrane-bounded organelle. [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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.566 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001378034.2. 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
	SNX25	NM_001378034.2	MANE Select	c.1091+1985C>T		intron	N/A	NP_001364963.1	A0A494C0S0
	SNX25	NM_001378032.2		c.1091+1985C>T		intron	N/A	NP_001364961.1
	SNX25	NM_001423234.1		c.1091+1985C>T		intron	N/A	NP_001410163.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SNX25	ENST00000652585.2	MANE Select	c.1091+1985C>T		intron	N/A	ENSP00000498676.1	A0A494C0S0
	SNX25	ENST00000504273.5	TSL:1	c.599+1985C>T		intron	N/A	ENSP00000426255.1	Q9H3E2-1
	SNX25	ENST00000927314.1		c.1091+1985C>T		intron	N/A	ENSP00000597373.1

Frequencies

GnomAD3 genomes AF: 0.424 AC: 64283 AN: 151724 Hom.: 13810 Cov.: 31

Gnomad AFR AF: 0.382

Gnomad AMI AF: 0.477

Gnomad AMR AF: 0.450

Gnomad ASJ AF: 0.453

Gnomad EAS AF: 0.583

Gnomad SAS AF: 0.426

Gnomad FIN AF: 0.369

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.438

Gnomad OTH AF: 0.417

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

GnomAD4 genome AF: 0.424 AC: 64352 AN: 151842 Hom.: 13831 Cov.: 31 AF XY: 0.421 AC XY: 31206 AN XY: 74180

African (AFR) AF: 0.382 AC: 15808 AN: 41414

American (AMR) AF: 0.451 AC: 6876 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.453 AC: 1571 AN: 3468

East Asian (EAS) AF: 0.583 AC: 3007 AN: 5154

South Asian (SAS) AF: 0.426 AC: 2051 AN: 4810

European-Finnish (FIN) AF: 0.369 AC: 3880 AN: 10504

Middle Eastern (MID) AF: 0.354 AC: 104 AN: 294

European-Non Finnish (NFE) AF: 0.438 AC: 29733 AN: 67924

Other (OTH) AF: 0.420 AC: 888 AN: 2112

Alfa AF: 0.432 Hom.: 7599

Bravo AF: 0.423

Asia WGS AF: 0.513 AC: 1784 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.58
DANN	Benign	0.81
PhyloP100		-1.0
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: rs2310160; hg19: chr4-186190294;