chr20-35021273-T-C
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_015638.3(TRPC4AP):āc.1135A>Gā(p.Met379Val) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000211 in 1,614,014 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. M379T) has been classified as Uncertain significance.
Frequency
Consequence
NM_015638.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TRPC4AP | NM_015638.3 | c.1135A>G | p.Met379Val | missense_variant | 9/19 | ENST00000252015.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRPC4AP | ENST00000252015.3 | c.1135A>G | p.Met379Val | missense_variant | 9/19 | 1 | NM_015638.3 | P4 | |
TRPC4AP | ENST00000451813.6 | c.1111A>G | p.Met371Val | missense_variant | 9/19 | 2 | A1 |
Frequencies
GnomAD3 genomes AF: 0.0000855 AC: 13AN: 152128Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000278 AC: 7AN: 251400Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135884
GnomAD4 exome AF: 0.0000144 AC: 21AN: 1461886Hom.: 0 Cov.: 31 AF XY: 0.0000165 AC XY: 12AN XY: 727246
GnomAD4 genome AF: 0.0000855 AC: 13AN: 152128Hom.: 0 Cov.: 32 AF XY: 0.000121 AC XY: 9AN XY: 74304
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 31, 2022 | The c.1135A>G (p.M379V) alteration is located in exon 9 (coding exon 9) of the TRPC4AP gene. This alteration results from a A to G substitution at nucleotide position 1135, causing the methionine (M) at amino acid position 379 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