1-98672141-C-T

Variant names:

• chr1-98672141-C-T
• rs9285629
• NM_015976.5:c.180+10230C>T

Variant summary

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

The NM_015976.5(SNX7):​c.180+10230C>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 152,112 control chromosomes in the GnomAD database, including 59,724 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 (59724 hom., cov: 31)
• Consequence: SNX7 NM_015976.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.537
• Publications: 1 publications found

Genes affected

SNX7 (HGNC:14971): (sorting nexin 7) This gene encodes a member of the sorting nexin family. Members of this family contain a phox (PX) domain, which is a phosphoinositide binding domain, and are involved in intracellular trafficking. This protein does not contain a coiled coil region like some family members, and its exact function is unknown. Alternative splicing results in multiple transcript variants. A related pseudogene has been identified on chromosome 11. [provided by RefSeq, Jun 2010]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.957 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SNX7	NM_015976.5	c.180+10230C>T		intron_variant	Intron 1 of 8	ENST00000306121.8	NP_057060.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SNX7	ENST00000306121.8	c.180+10230C>T		intron_variant	Intron 1 of 8	1	NM_015976.5	ENSP00000304429.3

Frequencies

GnomAD3 genomes AF: 0.877 AC: 133269 AN: 151994 Hom.: 59707 Cov.: 31

Gnomad AFR AF: 0.670

Gnomad AMI AF: 0.855

Gnomad AMR AF: 0.937

Gnomad ASJ AF: 0.978

Gnomad EAS AF: 0.908

Gnomad SAS AF: 0.961

Gnomad FIN AF: 0.950

Gnomad MID AF: 0.924

Gnomad NFE AF: 0.963

Gnomad OTH AF: 0.902

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

GnomAD4 genome AF: 0.876 AC: 133326 AN: 152112 Hom.: 59724 Cov.: 31 AF XY: 0.878 AC XY: 65317 AN XY: 74362

African (AFR) AF: 0.670 AC: 27762 AN: 41464

American (AMR) AF: 0.937 AC: 14316 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.978 AC: 3395 AN: 3470

East Asian (EAS) AF: 0.908 AC: 4678 AN: 5152

South Asian (SAS) AF: 0.961 AC: 4622 AN: 4810

European-Finnish (FIN) AF: 0.950 AC: 10078 AN: 10604

Middle Eastern (MID) AF: 0.922 AC: 271 AN: 294

European-Non Finnish (NFE) AF: 0.963 AC: 65526 AN: 68024

Other (OTH) AF: 0.902 AC: 1898 AN: 2104

Alfa AF: 0.891 Hom.: 3367

Bravo AF: 0.865

Asia WGS AF: 0.912 AC: 3171 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.5
DANN	Benign	0.70
PhyloP100		0.54
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: rs9285629; hg19: chr1-99137697;