chr12-26974066-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_016551.3(TM7SF3):āc.1612A>Gā(p.Ile538Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000112 in 1,614,054 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_016551.3 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 |
---|---|---|---|---|---|---|---|
TM7SF3 | NM_016551.3 | c.1612A>G | p.Ile538Val | missense_variant | 12/12 | ENST00000343028.9 | |
TM7SF3 | XM_017019463.3 | c.1702A>G | p.Ile568Val | missense_variant | 12/12 | ||
TM7SF3 | XM_047428990.1 | c.1549A>G | p.Ile517Val | missense_variant | 11/11 | ||
TM7SF3 | XM_005253391.5 | c.1459A>G | p.Ile487Val | missense_variant | 11/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TM7SF3 | ENST00000343028.9 | c.1612A>G | p.Ile538Val | missense_variant | 12/12 | 1 | NM_016551.3 | P1 | |
ENST00000500632.1 | n.960+1521T>C | intron_variant, non_coding_transcript_variant | 5 | ||||||
TM7SF3 | ENST00000544179.1 | downstream_gene_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152166Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251398Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135874
GnomAD4 exome AF: 0.0000103 AC: 15AN: 1461888Hom.: 0 Cov.: 30 AF XY: 0.00000688 AC XY: 5AN XY: 727246
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152166Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74346
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 14, 2023 | The c.1612A>G (p.I538V) alteration is located in exon 12 (coding exon 12) of the TM7SF3 gene. This alteration results from a A to G substitution at nucleotide position 1612, causing the isoleucine (I) at amino acid position 538 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