chr19-45216092-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001382422.1(EXOC3L2):c.2101C>T(p.Arg701Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000062 in 1,613,668 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R701H) has been classified as Uncertain significance.
Frequency
Consequence
NM_001382422.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EXOC3L2 | NM_001382422.1 | c.2101C>T | p.Arg701Cys | missense_variant | 11/12 | ENST00000413988.3 | |
BLOC1S3 | XR_007066811.1 | n.1527-584G>A | intron_variant, non_coding_transcript_variant | ||||
BLOC1S3 | XR_007066813.1 | n.1499-584G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EXOC3L2 | ENST00000413988.3 | c.2101C>T | p.Arg701Cys | missense_variant | 11/12 | 5 | NM_001382422.1 | P1 | |
MARK4 | ENST00000587566.5 | c.-276-42897G>A | intron_variant | 5 | |||||
BLOC1S3 | ENST00000591569.1 | n.283-584G>A | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 151966Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000160 AC: 4AN: 250688Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135692
GnomAD4 exome AF: 0.00000410 AC: 6AN: 1461702Hom.: 0 Cov.: 31 AF XY: 0.00000413 AC XY: 3AN XY: 727150
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 151966Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74240
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 06, 2022 | The c.922C>T (p.R308C) alteration is located in exon 9 (coding exon 8) of the EXOC3L2 gene. This alteration results from a C to T substitution at nucleotide position 922, causing the arginine (R) at amino acid position 308 to be replaced by a cysteine (C). 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