chr20-32143008-C-A
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 1P and 6B. PP2BP4_ModerateBS2
The NM_014742.4(TM9SF4):c.555C>A(p.Phe185Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000514 in 1,613,654 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_014742.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TM9SF4 | NM_014742.4 | c.555C>A | p.Phe185Leu | missense_variant | 6/18 | ENST00000398022.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TM9SF4 | ENST00000398022.7 | c.555C>A | p.Phe185Leu | missense_variant | 6/18 | 1 | NM_014742.4 | P1 | |
TM9SF4 | ENST00000217315.9 | c.504C>A | p.Phe168Leu | missense_variant | 6/18 | 2 |
Frequencies
GnomAD3 genomes AF: 0.000105 AC: 16AN: 152206Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.0000676 AC: 17AN: 251474Hom.: 0 AF XY: 0.0000956 AC XY: 13AN XY: 135914
GnomAD4 exome AF: 0.0000458 AC: 67AN: 1461448Hom.: 3 Cov.: 30 AF XY: 0.0000674 AC XY: 49AN XY: 727018
GnomAD4 genome AF: 0.000105 AC: 16AN: 152206Hom.: 1 Cov.: 32 AF XY: 0.000148 AC XY: 11AN XY: 74348
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 07, 2024 | The c.555C>A (p.F185L) alteration is located in exon 6 (coding exon 6) of the TM9SF4 gene. This alteration results from a C to A substitution at nucleotide position 555, causing the phenylalanine (F) at amino acid position 185 to be replaced by a leucine (L). 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