chr9-136377790-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.4037C>T(p.Ala1346Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000249 in 1,611,912 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.4037C>T | p.Ala1346Val | missense_variant | 22/24 | ENST00000684778.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SNAPC4 | ENST00000684778.1 | c.4037C>T | p.Ala1346Val | missense_variant | 22/24 | NM_003086.4 | P1 | ||
SNAPC4 | ENST00000298532.2 | c.4037C>T | p.Ala1346Val | missense_variant | 21/23 | 1 | P1 | ||
SNAPC4 | ENST00000637388.2 | c.4037C>T | p.Ala1346Val | missense_variant | 22/24 | 5 | P1 | ||
SNAPC4 | ENST00000689006.1 | c.*3250C>T | 3_prime_UTR_variant, NMD_transcript_variant | 22/24 |
Frequencies
GnomAD3 genomes AF: 0.000184 AC: 28AN: 152156Hom.: 1 Cov.: 34
GnomAD3 exomes AF: 0.000169 AC: 41AN: 242476Hom.: 0 AF XY: 0.000143 AC XY: 19AN XY: 132606
GnomAD4 exome AF: 0.000256 AC: 373AN: 1459640Hom.: 0 Cov.: 42 AF XY: 0.000227 AC XY: 165AN XY: 726140
GnomAD4 genome AF: 0.000184 AC: 28AN: 152272Hom.: 1 Cov.: 34 AF XY: 0.000107 AC XY: 8AN XY: 74456
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 17, 2021 | The c.4037C>T (p.A1346V) 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 4037, causing the alanine (A) at amino acid position 1346 to be replaced by a valine (V). 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