chr1-98695628-C-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_015976.5(SNX7):c.750C>A(p.Phe250Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00603 in 1,613,282 control chromosomes in the GnomAD database, including 58 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0045 ( 7 hom., cov: 32)
Exomes 𝑓: 0.0062 ( 51 hom. )
Consequence
SNX7
NM_015976.5 missense
NM_015976.5 missense
Scores
3
7
6
Clinical Significance
Conservation
PhyloP100: 2.13
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.011921674).
BP6
?
Variant 1-98695628-C-A is Benign according to our data. Variant chr1-98695628-C-A is described in ClinVar as [Benign]. Clinvar id is 719339.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
?
High Homozygotes in GnomAd at 7 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SNX7 | NM_015976.5 | c.750C>A | p.Phe250Leu | missense_variant | 5/9 | ENST00000306121.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SNX7 | ENST00000306121.8 | c.750C>A | p.Phe250Leu | missense_variant | 5/9 | 1 | NM_015976.5 | P1 | |
SNX7 | ENST00000528824.1 | c.*570C>A | 3_prime_UTR_variant, NMD_transcript_variant | 6/9 | 1 | ||||
SNX7 | ENST00000529992.5 | c.585C>A | p.Phe195Leu | missense_variant | 4/8 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00455 AC: 692AN: 152014Hom.: 7 Cov.: 32
GnomAD3 genomes
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GnomAD3 exomes AF: 0.00481 AC: 1210AN: 251364Hom.: 10 AF XY: 0.00504 AC XY: 685AN XY: 135896
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GnomAD4 exome AF: 0.00619 AC: 9041AN: 1461148Hom.: 51 Cov.: 30 AF XY: 0.00605 AC XY: 4398AN XY: 726936
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GnomAD4 genome ? AF: 0.00454 AC: 691AN: 152134Hom.: 7 Cov.: 32 AF XY: 0.00510 AC XY: 379AN XY: 74368
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22
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52
ExAC
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537
Asia WGS
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Mar 06, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
T
BayesDel_noAF
Uncertain
Cadd
Uncertain
Dann
Uncertain
DEOGEN2
Benign
T;.
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D;D
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationTaster
Benign
D;D;D
PrimateAI
Uncertain
T
PROVEAN
Pathogenic
D;D
REVEL
Uncertain
Sift
Benign
T;T
Sift4G
Uncertain
D;D
Polyphen
D;D
Vest4
MutPred
Gain of MoRF binding (P = 0.1485);.;
MVP
MPC
0.52
ClinPred
T
GERP RS
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at