1-98757952-C-T

Variant names:

• chr1-98757952-C-T
• rs12406053
• NM_015976.5:c.1279-2102C>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.1279-2102C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.263 in 151,910 control chromosomes in the GnomAD database, including 5,569 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 0.26 (5569 hom., cov: 32)
• Consequence: SNX7 NM_015976.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.230
• Publications: 3 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=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.296 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SNX7	NM_015976.5	c.1279-2102C>T		intron_variant	Intron 8 of 8	ENST00000306121.8	NP_057060.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SNX7	ENST00000306121.8	c.1279-2102C>T		intron_variant	Intron 8 of 8	1	NM_015976.5	ENSP00000304429.3
SNX7	ENST00000528824.1	n.*946-2102C>T		intron_variant	Intron 8 of 8	1		ENSP00000435172.1
SNX7	ENST00000529992.5	c.1114-2102C>T		intron_variant	Intron 7 of 7	2		ENSP00000434731.1

Frequencies

GnomAD3 genomes AF: 0.263 AC: 39906 AN: 151792 Hom.: 5563 Cov.: 32

Gnomad AFR AF: 0.235

Gnomad AMI AF: 0.353

Gnomad AMR AF: 0.252

Gnomad ASJ AF: 0.275

Gnomad EAS AF: 0.0585

Gnomad SAS AF: 0.309

Gnomad FIN AF: 0.262

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.293

Gnomad OTH AF: 0.258

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

GnomAD4 genome AF: 0.263 AC: 39944 AN: 151910 Hom.: 5569 Cov.: 32 AF XY: 0.263 AC XY: 19504 AN XY: 74250

African (AFR) AF: 0.236 AC: 9767 AN: 41436

American (AMR) AF: 0.252 AC: 3834 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.275 AC: 955 AN: 3468

East Asian (EAS) AF: 0.0580 AC: 299 AN: 5152

South Asian (SAS) AF: 0.309 AC: 1491 AN: 4824

European-Finnish (FIN) AF: 0.262 AC: 2772 AN: 10574

Middle Eastern (MID) AF: 0.306 AC: 90 AN: 294

European-Non Finnish (NFE) AF: 0.293 AC: 19877 AN: 67904

Other (OTH) AF: 0.255 AC: 539 AN: 2110

Alfa AF: 0.267 Hom.: 5182

Bravo AF: 0.259

Asia WGS AF: 0.172 AC: 598 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	5.0
DANN	Benign	0.56
PhyloP100		0.23
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: rs12406053; hg19: chr1-99223508;