chr16-84482597-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_020947.4(MEAK7):c.1072G>A(p.Gly358Arg) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000322 in 1,614,154 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G358V) has been classified as Uncertain significance.
Frequency
Consequence
NM_020947.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MEAK7 | NM_020947.4 | c.1072G>A | p.Gly358Arg | missense_variant | 6/8 | ENST00000343629.11 | |
MEAK7 | XM_005256075.3 | c.1072G>A | p.Gly358Arg | missense_variant | 7/9 | ||
MEAK7 | XM_017023511.2 | c.1072G>A | p.Gly358Arg | missense_variant | 6/8 | ||
MEAK7 | XM_047434410.1 | c.1072G>A | p.Gly358Arg | missense_variant | 6/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MEAK7 | ENST00000343629.11 | c.1072G>A | p.Gly358Arg | missense_variant | 6/8 | 1 | NM_020947.4 | P1 | |
MEAK7 | ENST00000566995.5 | c.*486G>A | 3_prime_UTR_variant, NMD_transcript_variant | 7/9 | 5 | ||||
MEAK7 | ENST00000570036.5 | c.*1127G>A | 3_prime_UTR_variant, NMD_transcript_variant | 7/9 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.000112 AC: 17AN: 152218Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000875 AC: 22AN: 251352Hom.: 0 AF XY: 0.0000957 AC XY: 13AN XY: 135836
GnomAD4 exome AF: 0.0000233 AC: 34AN: 1461818Hom.: 0 Cov.: 31 AF XY: 0.0000275 AC XY: 20AN XY: 727212
GnomAD4 genome ? AF: 0.000118 AC: 18AN: 152336Hom.: 0 Cov.: 33 AF XY: 0.0000805 AC XY: 6AN XY: 74492
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 01, 2023 | The c.1072G>A (p.G358R) alteration is located in exon 6 (coding exon 5) of the TLDC1 gene. This alteration results from a G to A substitution at nucleotide position 1072, causing the glycine (G) at amino acid position 358 to be replaced by an arginine (R). 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