chr3-140459568-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_022131.3(CLSTN2):c.1021A>G(p.Thr341Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000135 in 1,613,962 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_022131.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CLSTN2 | NM_022131.3 | c.1021A>G | p.Thr341Ala | missense_variant | 7/17 | ENST00000458420.7 | |
LOC105374132 | XR_007096117.1 | n.49-4815T>C | intron_variant, non_coding_transcript_variant | ||||
CLSTN2 | XM_017007022.3 | c.946A>G | p.Thr316Ala | missense_variant | 7/17 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CLSTN2 | ENST00000458420.7 | c.1021A>G | p.Thr341Ala | missense_variant | 7/17 | 1 | NM_022131.3 | P1 | |
ENST00000503357.1 | n.100+684T>C | intron_variant, non_coding_transcript_variant | 3 | ||||||
CLSTN2 | ENST00000511524.1 | n.1209A>G | non_coding_transcript_exon_variant | 7/11 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.000138 AC: 21AN: 152118Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000243 AC: 61AN: 250982Hom.: 0 AF XY: 0.000251 AC XY: 34AN XY: 135630
GnomAD4 exome AF: 0.000135 AC: 197AN: 1461844Hom.: 1 Cov.: 32 AF XY: 0.000133 AC XY: 97AN XY: 727226
GnomAD4 genome ? AF: 0.000138 AC: 21AN: 152118Hom.: 0 Cov.: 33 AF XY: 0.000162 AC XY: 12AN XY: 74288
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 15, 2021 | The c.1021A>G (p.T341A) alteration is located in exon 7 (coding exon 7) of the CLSTN2 gene. This alteration results from a A to G substitution at nucleotide position 1021, causing the threonine (T) at amino acid position 341 to be replaced by an alanine (A). 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