7-44582121-C-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_182547.4(TMED4):c.86G>C(p.Gly29Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00141 in 1,555,898 control chromosomes in the GnomAD database, including 1 homozygotes. 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 Uncertain significance (★).
Frequency
Consequence
NM_182547.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000893 AC: 136AN: 152244Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000784 AC: 126AN: 160620Hom.: 0 AF XY: 0.000724 AC XY: 62AN XY: 85596
GnomAD4 exome AF: 0.00146 AC: 2051AN: 1403536Hom.: 1 Cov.: 32 AF XY: 0.00136 AC XY: 943AN XY: 692988
GnomAD4 genome AF: 0.000893 AC: 136AN: 152362Hom.: 0 Cov.: 33 AF XY: 0.000940 AC XY: 70AN XY: 74504
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.86G>C (p.G29A) alteration is located in exon 1 (coding exon 1) of the TMED4 gene. This alteration results from a G to C substitution at nucleotide position 86, causing the glycine (G) at amino acid position 29 to be replaced by an alanine (A). 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