rs9727115

Variant names:

• chr1-98711697-G-A
• rs9727115
• NM_015976.5:c.1125+9794G>A

Variant summary

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

The NM_015976.5(SNX7):​c.1125+9794G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.366 in 152,016 control chromosomes in the GnomAD database, including 10,390 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 0.37 (10390 hom., cov: 32)
• Consequence: SNX7 NM_015976.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.531
• Publications: 17 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.401 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SNX7	NM_015976.5	c.1125+9794G>A		intron_variant	Intron 7 of 8	ENST00000306121.8	NP_057060.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SNX7	ENST00000306121.8	c.1125+9794G>A		intron_variant	Intron 7 of 8	1	NM_015976.5	ENSP00000304429.3
SNX7	ENST00000528824.1	n.*945+9794G>A		intron_variant	Intron 8 of 8	1		ENSP00000435172.1
SNX7	ENST00000529992.5	c.960+9794G>A		intron_variant	Intron 6 of 7	2		ENSP00000434731.1

Frequencies

GnomAD3 genomes AF: 0.366 AC: 55618 AN: 151898 Hom.: 10387 Cov.: 32

Gnomad AFR AF: 0.407

Gnomad AMI AF: 0.293

Gnomad AMR AF: 0.356

Gnomad ASJ AF: 0.418

Gnomad EAS AF: 0.397

Gnomad SAS AF: 0.320

Gnomad FIN AF: 0.309

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.351

Gnomad OTH AF: 0.391

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

GnomAD4 genome AF: 0.366 AC: 55633 AN: 152016 Hom.: 10390 Cov.: 32 AF XY: 0.362 AC XY: 26910 AN XY: 74288

African (AFR) AF: 0.407 AC: 16859 AN: 41462

American (AMR) AF: 0.355 AC: 5425 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.418 AC: 1452 AN: 3470

East Asian (EAS) AF: 0.398 AC: 2050 AN: 5152

South Asian (SAS) AF: 0.319 AC: 1539 AN: 4822

European-Finnish (FIN) AF: 0.309 AC: 3268 AN: 10572

Middle Eastern (MID) AF: 0.373 AC: 109 AN: 292

European-Non Finnish (NFE) AF: 0.351 AC: 23841 AN: 67956

Other (OTH) AF: 0.390 AC: 824 AN: 2114

Alfa AF: 0.361 Hom.: 20048

Bravo AF: 0.369

Asia WGS AF: 0.387 AC: 1347 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.0
DANN	Benign	0.67
PhyloP100		0.53
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: rs9727115; hg19: chr1-99177253;