chr1-98733890-T-C

Variant names:

• chr1-98733890-T-C
• rs12057921
• NM_015976.5:c.1126-4347T>C

Variant summary

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

The NM_015976.5(SNX7):​c.1126-4347T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.276 in 152,050 control chromosomes in the GnomAD database, including 6,133 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 0.28 (6133 hom., cov: 32)
• Consequence: SNX7 NM_015976.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.907
• 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=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.295 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SNX7	NM_015976.5	c.1126-4347T>C		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.1126-4347T>C		intron_variant	Intron 7 of 8	1	NM_015976.5	ENSP00000304429.3
SNX7	ENST00000528824.1	n.*946-26164T>C		intron_variant	Intron 8 of 8	1		ENSP00000435172.1
SNX7	ENST00000529992.5	c.961-4347T>C		intron_variant	Intron 6 of 7	2		ENSP00000434731.1

Frequencies

GnomAD3 genomes AF: 0.276 AC: 41994 AN: 151932 Hom.: 6123 Cov.: 32

Gnomad AFR AF: 0.280

Gnomad AMI AF: 0.353

Gnomad AMR AF: 0.257

Gnomad ASJ AF: 0.275

Gnomad EAS AF: 0.0581

Gnomad SAS AF: 0.308

Gnomad FIN AF: 0.262

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.294

Gnomad OTH AF: 0.268

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

GnomAD4 genome AF: 0.276 AC: 42035 AN: 152050 Hom.: 6133 Cov.: 32 AF XY: 0.275 AC XY: 20476 AN XY: 74364

African (AFR) AF: 0.281 AC: 11652 AN: 41480

American (AMR) AF: 0.257 AC: 3918 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.275 AC: 951 AN: 3464

East Asian (EAS) AF: 0.0577 AC: 298 AN: 5168

South Asian (SAS) AF: 0.308 AC: 1483 AN: 4814

European-Finnish (FIN) AF: 0.262 AC: 2781 AN: 10604

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.294 AC: 19977 AN: 67940

Other (OTH) AF: 0.265 AC: 561 AN: 2114

Alfa AF: 0.177 Hom.: 400

Bravo AF: 0.274

Asia WGS AF: 0.176 AC: 615 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.53
PhyloP100		-0.91
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: rs12057921; hg19: chr1-99199446;