1-98698839-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_015976.5(SNX7):c.972G>A(p.Met324Ile) variant causes a missense change. The variant allele was found at a frequency of 0.000496 in 1,613,748 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.00033 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00051 ( 0 hom. )
Consequence
SNX7
NM_015976.5 missense
NM_015976.5 missense
Scores
1
16
Clinical Significance
Conservation
PhyloP100: 4.36
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 Likely_benign. Variant got -2 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (MetaRNN=0.059732765).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SNX7 | NM_015976.5 | c.972G>A | p.Met324Ile | missense_variant | 6/9 | ENST00000306121.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SNX7 | ENST00000306121.8 | c.972G>A | p.Met324Ile | missense_variant | 6/9 | 1 | NM_015976.5 | P1 | |
SNX7 | ENST00000528824.1 | c.*792G>A | 3_prime_UTR_variant, NMD_transcript_variant | 7/9 | 1 | ||||
SNX7 | ENST00000529992.5 | c.807G>A | p.Met269Ile | missense_variant | 5/8 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.000329 AC: 50AN: 152110Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000291 AC: 73AN: 251264Hom.: 0 AF XY: 0.000361 AC XY: 49AN XY: 135782
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GnomAD4 exome AF: 0.000513 AC: 750AN: 1461638Hom.: 0 Cov.: 36 AF XY: 0.000543 AC XY: 395AN XY: 727128
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GnomAD4 genome ? AF: 0.000329 AC: 50AN: 152110Hom.: 0 Cov.: 32 AF XY: 0.000256 AC XY: 19AN XY: 74292
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 17, 2023 | The c.972G>A (p.M324I) alteration is located in exon 6 (coding exon 6) of the SNX7 gene. This alteration results from a G to A substitution at nucleotide position 972, causing the methionine (M) at amino acid position 324 to be replaced by an isoleucine (I). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
DEOGEN2
Benign
T;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T;T
M_CAP
Benign
T
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationTaster
Benign
N;N;N
PrimateAI
Benign
T
PROVEAN
Benign
N;N
REVEL
Benign
Sift
Benign
T;T
Sift4G
Benign
T;T
Polyphen
B;B
Vest4
MutPred
Loss of disorder (P = 0.0762);.;
MVP
MPC
0.098
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