rs760861421
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001546.4(ID4):c.389C>G(p.Thr130Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000154 in 1,553,816 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 Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T130I) has been classified as Uncertain significance.
Frequency
Consequence
NM_001546.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 151926Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000791 AC: 13AN: 164350Hom.: 0 AF XY: 0.0000996 AC XY: 9AN XY: 90358
GnomAD4 exome AF: 0.0000157 AC: 22AN: 1401890Hom.: 0 Cov.: 32 AF XY: 0.0000144 AC XY: 10AN XY: 693908
GnomAD4 genome AF: 0.0000132 AC: 2AN: 151926Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74208
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.389C>G (p.T130S) alteration is located in exon 1 (coding exon 1) of the ID4 gene. This alteration results from a C to G substitution at nucleotide position 389, causing the threonine (T) at amino acid position 130 to be replaced by a serine (S). 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