7-17803526-C-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_015132.5(SNX13):c.2119G>T(p.Val707Phe) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000391 in 1,612,152 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_015132.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SNX13 | NM_015132.5 | c.2119G>T | p.Val707Phe | missense_variant | Exon 21 of 26 | ENST00000428135.7 | NP_055947.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152136Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000162 AC: 4AN: 246170Hom.: 0 AF XY: 0.0000150 AC XY: 2AN XY: 133506
GnomAD4 exome AF: 0.0000397 AC: 58AN: 1460016Hom.: 0 Cov.: 30 AF XY: 0.0000386 AC XY: 28AN XY: 726160
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152136Hom.: 0 Cov.: 31 AF XY: 0.0000269 AC XY: 2AN XY: 74312
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.2119G>T (p.V707F) alteration is located in exon 21 (coding exon 21) of the SNX13 gene. This alteration results from a G to T substitution at nucleotide position 2119, causing the valine (V) at amino acid position 707 to be replaced by a phenylalanine (F). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at