chr20-32161283-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 3P and 1B. PM2PP2BP4
The NM_014742.4(TM9SF4):c.1697G>A(p.Arg566His) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000545 in 1,613,738 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 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 Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TM9SF4 | NM_014742.4 | c.1697G>A | p.Arg566His | missense_variant | 17/18 | ENST00000398022.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TM9SF4 | ENST00000398022.7 | c.1697G>A | p.Arg566His | missense_variant | 17/18 | 1 | NM_014742.4 | P1 | |
TM9SF4 | ENST00000217315.9 | c.1646G>A | p.Arg549His | missense_variant | 17/18 | 2 | |||
TM9SF4 | ENST00000479591.1 | n.191G>A | non_coding_transcript_exon_variant | 1/2 | 2 | ||||
TM9SF4 | ENST00000495749.1 | n.977G>A | non_coding_transcript_exon_variant | 2/3 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000460 AC: 7AN: 152152Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000557 AC: 14AN: 251442Hom.: 0 AF XY: 0.0000736 AC XY: 10AN XY: 135902
GnomAD4 exome AF: 0.0000554 AC: 81AN: 1461468Hom.: 0 Cov.: 30 AF XY: 0.0000495 AC XY: 36AN XY: 727038
GnomAD4 genome ? AF: 0.0000460 AC: 7AN: 152270Hom.: 0 Cov.: 32 AF XY: 0.0000672 AC XY: 5AN XY: 74454
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 06, 2023 | The c.1697G>A (p.R566H) alteration is located in exon 17 (coding exon 17) of the TM9SF4 gene. This alteration results from a G to A substitution at nucleotide position 1697, causing the arginine (R) at amino acid position 566 to be replaced by a histidine (H). 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