chr12-26974152-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_016551.3(TM7SF3):c.1526G>A(p.Arg509Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000246 in 1,461,870 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_016551.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TM7SF3 | NM_016551.3 | c.1526G>A | p.Arg509Gln | missense_variant | 12/12 | ENST00000343028.9 | NP_057635.1 | |
TM7SF3 | XM_017019463.3 | c.1616G>A | p.Arg539Gln | missense_variant | 12/12 | XP_016874952.1 | ||
TM7SF3 | XM_047428990.1 | c.1463G>A | p.Arg488Gln | missense_variant | 11/11 | XP_047284946.1 | ||
TM7SF3 | XM_005253391.5 | c.1373G>A | p.Arg458Gln | missense_variant | 11/11 | XP_005253448.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TM7SF3 | ENST00000343028.9 | c.1526G>A | p.Arg509Gln | missense_variant | 12/12 | 1 | NM_016551.3 | ENSP00000342322 | P1 | |
ENST00000500632.1 | n.960+1607C>T | intron_variant, non_coding_transcript_variant | 5 | |||||||
TM7SF3 | ENST00000544179.1 | n.356G>A | non_coding_transcript_exon_variant | 2/2 | 2 | |||||
TM7SF3 | ENST00000545344.5 | downstream_gene_variant | 3 | ENSP00000445756 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000358 AC: 9AN: 251350Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135844
GnomAD4 exome AF: 0.0000246 AC: 36AN: 1461870Hom.: 0 Cov.: 30 AF XY: 0.0000206 AC XY: 15AN XY: 727238
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 12, 2024 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at