rs2019213

Variant names:

• chr1-98760071-G-A
• rs2019213
• NM_015976.5:c.1296G>A

Your query was ambiguous. Multiple possible variants found:

• chr1-98760071-G-A
• chr1-98760071-G-C
• chr1-98760071-G-T

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The NM_015976.5(SNX7):​c.1296G>A​(p.Glu432Glu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.967 in 1,605,966 control chromosomes in the GnomAD database, including 753,696 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 0.94 (67798 hom., cov: 31)
  • Exomes 𝑓: 0.97 (685898 hom.)
• Consequence: SNX7 NM_015976.5 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00400
• Publications: 18 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 -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.58).
• BP7: Synonymous conserved (PhyloP=0.004 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.981 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SNX7	NM_015976.5	c.1296G>A	p.Glu432Glu	synonymous_variant	Exon 9 of 9	ENST00000306121.8	NP_057060.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SNX7	ENST00000306121.8	c.1296G>A	p.Glu432Glu	synonymous_variant	Exon 9 of 9	1	NM_015976.5	ENSP00000304429.3
SNX7	ENST00000528824.1	n.*963G>A		non_coding_transcript_exon_variant	Exon 9 of 9	1		ENSP00000435172.1
SNX7	ENST00000528824.1	n.*963G>A		3_prime_UTR_variant	Exon 9 of 9	1		ENSP00000435172.1
SNX7	ENST00000529992.5	c.1131G>A	p.Glu377Glu	synonymous_variant	Exon 8 of 8	2		ENSP00000434731.1

Frequencies

GnomAD3 genomes AF: 0.942 AC: 143137 AN: 151964 Hom.: 67774 Cov.: 31

Gnomad AFR AF: 0.897

Gnomad AMI AF: 0.968

Gnomad AMR AF: 0.919

Gnomad ASJ AF: 0.989

Gnomad EAS AF: 0.658

Gnomad SAS AF: 0.955

Gnomad FIN AF: 0.971

Gnomad MID AF: 0.978

Gnomad NFE AF: 0.987

Gnomad OTH AF: 0.951

GnomAD2 exomes AF: 0.934 AC: 233974 AN: 250536 AF XY: 0.942

Gnomad AFR exome AF: 0.895

Gnomad AMR exome AF: 0.850

Gnomad ASJ exome AF: 0.989

Gnomad EAS exome AF: 0.651

Gnomad FIN exome AF: 0.973

Gnomad NFE exome AF: 0.987

Gnomad OTH exome AF: 0.957

GnomAD4 exome AF: 0.969 AC: 1409254 AN: 1453884 Hom.: 685898 Cov.: 36 AF XY: 0.970 AC XY: 702226 AN XY: 723768

African (AFR) AF: 0.893 AC: 29656 AN: 33218

American (AMR) AF: 0.857 AC: 38203 AN: 44578

Ashkenazi Jewish (ASJ) AF: 0.988 AC: 25704 AN: 26020

East Asian (EAS) AF: 0.645 AC: 25517 AN: 39558

South Asian (SAS) AF: 0.971 AC: 83586 AN: 86080

European-Finnish (FIN) AF: 0.974 AC: 52018 AN: 53388

Middle Eastern (MID) AF: 0.984 AC: 5660 AN: 5754

European-Non Finnish (NFE) AF: 0.987 AC: 1091154 AN: 1105172

Other (OTH) AF: 0.961 AC: 57756 AN: 60116

GnomAD4 genome AF: 0.942 AC: 143216 AN: 152082 Hom.: 67798 Cov.: 31 AF XY: 0.939 AC XY: 69767 AN XY: 74332

African (AFR) AF: 0.897 AC: 37233 AN: 41502

American (AMR) AF: 0.918 AC: 14010 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.989 AC: 3432 AN: 3470

East Asian (EAS) AF: 0.658 AC: 3370 AN: 5122

South Asian (SAS) AF: 0.954 AC: 4603 AN: 4826

European-Finnish (FIN) AF: 0.971 AC: 10308 AN: 10620

Middle Eastern (MID) AF: 0.976 AC: 287 AN: 294

European-Non Finnish (NFE) AF: 0.987 AC: 67084 AN: 67966

Other (OTH) AF: 0.950 AC: 2006 AN: 2112

Alfa AF: 0.965 Hom.: 240377

Bravo AF: 0.931

Asia WGS AF: 0.831 AC: 2891 AN: 3476

EpiCase AF: 0.986

EpiControl AF: 0.987

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.58
CADD	Benign	3.4
DANN	Benign	0.46
PhyloP100		0.0040
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.040		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: rs2019213; hg19: chr1-99225627; COSMIC: COSV60267904;