17-28959040-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_178860.5(SEZ6):c.2092G>A(p.Val698Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000633 in 1,612,232 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (no stars).
Frequency
Consequence
NM_178860.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SEZ6 | NM_178860.5 | c.2092G>A | p.Val698Ile | missense_variant | 10/17 | ENST00000317338.17 | |
LOC105371716 | XR_001752822.2 | n.1807+5632C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SEZ6 | ENST00000317338.17 | c.2092G>A | p.Val698Ile | missense_variant | 10/17 | 1 | NM_178860.5 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152208Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000142 AC: 35AN: 247252Hom.: 0 AF XY: 0.000201 AC XY: 27AN XY: 134136
GnomAD4 exome AF: 0.0000671 AC: 98AN: 1460024Hom.: 0 Cov.: 32 AF XY: 0.0000936 AC XY: 68AN XY: 726194
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152208Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74358
ClinVar
Submissions by phenotype
Nonsyndromic hearing impairment Uncertain:1
Uncertain significance, no assertion criteria provided | clinical testing | Center for Statistical Genetics, Columbia University | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at