9-112764903-C-T

Variant names:

• chr9-112764903-C-T
• rs1891403
• NM_001012994.2:c.156+13746C>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001012994.2(SNX30):​c.156+13746C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.876 in 152,174 control chromosomes in the GnomAD database, including 58,531 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 0.88 (58531 hom., cov: 32)
• Consequence: SNX30 NM_001012994.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0340

Genes affected

SNX30 (HGNC:23685): (sorting nexin family member 30) Predicted to enable phosphatidylinositol binding activity. Predicted to be involved in protein transport. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.898 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SNX30	NM_001012994.2	c.156+13746C>T		intron_variant	Intron 1 of 8	ENST00000374232.8	NP_001013012.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SNX30	ENST00000374232.8	c.156+13746C>T		intron_variant	Intron 1 of 8	5	NM_001012994.2	ENSP00000363349.3

Frequencies

GnomAD3 genomes AF: 0.876 AC: 133207 AN: 152056 Hom.: 58504 Cov.: 32

Gnomad AFR AF: 0.807

Gnomad AMI AF: 0.966

Gnomad AMR AF: 0.892

Gnomad ASJ AF: 0.899

Gnomad EAS AF: 0.881

Gnomad SAS AF: 0.914

Gnomad FIN AF: 0.906

Gnomad MID AF: 0.915

Gnomad NFE AF: 0.904

Gnomad OTH AF: 0.890

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

GnomAD4 genome AF: 0.876 AC: 133291 AN: 152174 Hom.: 58531 Cov.: 32 AF XY: 0.876 AC XY: 65202 AN XY: 74402

Gnomad4 AFR AF: 0.807

Gnomad4 AMR AF: 0.892

Gnomad4 ASJ AF: 0.899

Gnomad4 EAS AF: 0.881

Gnomad4 SAS AF: 0.914

Gnomad4 FIN AF: 0.906

Gnomad4 NFE AF: 0.904

Gnomad4 OTH AF: 0.890

Alfa AF: 0.898 Hom.: 79649

Bravo AF: 0.870

Asia WGS AF: 0.893 AC: 3104 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.3
DANN	Benign	0.46

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: rs1891403; hg19: chr9-115527183;