chr9-136377941-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_003086.4(SNAPC4):c.3886C>T(p.Leu1296Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000111 in 1,606,848 control chromosomes in the GnomAD database, including 1 homozygotes. 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.3886C>T | p.Leu1296Phe | missense_variant | 22/24 | ENST00000684778.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SNAPC4 | ENST00000684778.1 | c.3886C>T | p.Leu1296Phe | missense_variant | 22/24 | NM_003086.4 | P1 | ||
SNAPC4 | ENST00000298532.2 | c.3886C>T | p.Leu1296Phe | missense_variant | 21/23 | 1 | P1 | ||
SNAPC4 | ENST00000637388.2 | c.3886C>T | p.Leu1296Phe | missense_variant | 22/24 | 5 | P1 | ||
SNAPC4 | ENST00000689006.1 | c.*3099C>T | 3_prime_UTR_variant, NMD_transcript_variant | 22/24 |
Frequencies
GnomAD3 genomes ? AF: 0.000171 AC: 26AN: 152124Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000180 AC: 42AN: 233328Hom.: 0 AF XY: 0.000155 AC XY: 20AN XY: 128764
GnomAD4 exome AF: 0.000104 AC: 152AN: 1454724Hom.: 1 Cov.: 42 AF XY: 0.000101 AC XY: 73AN XY: 723058
GnomAD4 genome ? AF: 0.000171 AC: 26AN: 152124Hom.: 0 Cov.: 33 AF XY: 0.000175 AC XY: 13AN XY: 74310
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 27, 2023 | The c.3886C>T (p.L1296F) alteration is located in exon 21 (coding exon 21) of the SNAPC4 gene. This alteration results from a C to T substitution at nucleotide position 3886, causing the leucine (L) at amino acid position 1296 to be replaced by a phenylalanine (F). 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