chr7-100466996-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_030935.5(TSC22D4):c.1151G>A(p.Arg384Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000119 in 1,597,928 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_030935.5 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: 0.0000394 AC: 6AN: 152240Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000320 AC: 7AN: 219024Hom.: 0 AF XY: 0.0000167 AC XY: 2AN XY: 119448
GnomAD4 exome AF: 0.00000899 AC: 13AN: 1445688Hom.: 0 Cov.: 30 AF XY: 0.00000557 AC XY: 4AN XY: 717834
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152240Hom.: 0 Cov.: 32 AF XY: 0.0000672 AC XY: 5AN XY: 74378
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1151G>A (p.R384Q) alteration is located in exon 5 (coding exon 4) of the TSC22D4 gene. This alteration results from a G to A substitution at nucleotide position 1151, causing the arginine (R) at amino acid position 384 to be replaced by a glutamine (Q). 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