rs35296149
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000306121.8(SNX7):c.367T>A(p.Ser123Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0272 in 1,600,472 control chromosomes in the GnomAD database, including 3,594 homozygotes. In-silico tool predicts a benign outcome for this variant. 11/17 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
ENST00000306121.8 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SNX7 | NM_015976.5 | c.367T>A | p.Ser123Thr | missense_variant | 3/9 | ENST00000306121.8 | NP_057060.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SNX7 | ENST00000306121.8 | c.367T>A | p.Ser123Thr | missense_variant | 3/9 | 1 | NM_015976.5 | ENSP00000304429 | P1 | |
SNX7 | ENST00000528824.1 | c.*187T>A | 3_prime_UTR_variant, NMD_transcript_variant | 4/9 | 1 | ENSP00000435172 | ||||
SNX7 | ENST00000529992.5 | c.367T>A | p.Ser123Thr | missense_variant | 3/8 | 2 | ENSP00000434731 | |||
SNX7 | ENST00000454199.1 | c.175T>A | p.Ser59Thr | missense_variant | 3/4 | 4 | ENSP00000388266 |
Frequencies
GnomAD3 genomes AF: 0.0319 AC: 4845AN: 152036Hom.: 373 Cov.: 32
GnomAD3 exomes AF: 0.0586 AC: 14413AN: 245792Hom.: 1518 AF XY: 0.0527 AC XY: 7010AN XY: 133140
GnomAD4 exome AF: 0.0267 AC: 38674AN: 1448318Hom.: 3217 Cov.: 29 AF XY: 0.0264 AC XY: 19042AN XY: 721026
GnomAD4 genome AF: 0.0320 AC: 4864AN: 152154Hom.: 377 Cov.: 32 AF XY: 0.0355 AC XY: 2642AN XY: 74378
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at