9-136377829-A-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_003086.4(SNAPC4):c.3998T>G(p.Val1333Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000261 in 1,611,380 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_003086.4 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 |
---|---|---|---|---|---|---|---|
SNAPC4 | NM_003086.4 | c.3998T>G | p.Val1333Gly | missense_variant | 22/24 | ENST00000684778.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SNAPC4 | ENST00000684778.1 | c.3998T>G | p.Val1333Gly | missense_variant | 22/24 | NM_003086.4 | P1 | ||
SNAPC4 | ENST00000298532.2 | c.3998T>G | p.Val1333Gly | missense_variant | 21/23 | 1 | P1 | ||
SNAPC4 | ENST00000637388.2 | c.3998T>G | p.Val1333Gly | missense_variant | 22/24 | 5 | P1 | ||
SNAPC4 | ENST00000689006.1 | c.*3211T>G | 3_prime_UTR_variant, NMD_transcript_variant | 22/24 |
Frequencies
GnomAD3 genomes ? AF: 0.0000723 AC: 11AN: 152046Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000125 AC: 3AN: 240502Hom.: 0 AF XY: 0.0000152 AC XY: 2AN XY: 131848
GnomAD4 exome AF: 0.0000192 AC: 28AN: 1459216Hom.: 0 Cov.: 41 AF XY: 0.0000138 AC XY: 10AN XY: 725928
GnomAD4 genome ? AF: 0.0000920 AC: 14AN: 152164Hom.: 0 Cov.: 33 AF XY: 0.000121 AC XY: 9AN XY: 74394
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 08, 2024 | The c.3998T>G (p.V1333G) alteration is located in exon 21 (coding exon 21) of the SNAPC4 gene. This alteration results from a T to G substitution at nucleotide position 3998, causing the valine (V) at amino acid position 1333 to be replaced by a glycine (G). 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