rs17348572
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_022131.3(CLSTN2):āc.992T>Cā(p.Ile331Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0494 in 1,613,962 control chromosomes in the GnomAD database, including 2,107 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_022131.3 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 | UniProt |
---|---|---|---|---|---|---|---|
CLSTN2 | NM_022131.3 | c.992T>C | p.Ile331Thr | missense_variant | 7/17 | ENST00000458420.7 | |
LOC105374132 | XR_007096117.1 | n.49-4786A>G | intron_variant, non_coding_transcript_variant | ||||
CLSTN2 | XM_017007022.3 | c.917T>C | p.Ile306Thr | missense_variant | 7/17 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CLSTN2 | ENST00000458420.7 | c.992T>C | p.Ile331Thr | missense_variant | 7/17 | 1 | NM_022131.3 | P1 | |
ENST00000503357.1 | n.100+713A>G | intron_variant, non_coding_transcript_variant | 3 | ||||||
CLSTN2 | ENST00000511524.1 | n.1180T>C | non_coding_transcript_exon_variant | 7/11 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0399 AC: 6063AN: 152132Hom.: 146 Cov.: 32
GnomAD3 exomes AF: 0.0414 AC: 10382AN: 250710Hom.: 236 AF XY: 0.0425 AC XY: 5761AN XY: 135466
GnomAD4 exome AF: 0.0504 AC: 73739AN: 1461712Hom.: 1961 Cov.: 32 AF XY: 0.0503 AC XY: 36547AN XY: 727150
GnomAD4 genome ? AF: 0.0398 AC: 6064AN: 152250Hom.: 146 Cov.: 32 AF XY: 0.0399 AC XY: 2972AN XY: 74436
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at