4-105682944-A-G
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_020395.4(INTS12):āc.1178T>Cā(p.Leu393Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000558 in 1,614,000 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 (ā ).
Frequency
Consequence
NM_020395.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
INTS12 | NM_020395.4 | c.1178T>C | p.Leu393Ser | missense_variant | 8/8 | ENST00000340139.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
INTS12 | ENST00000340139.10 | c.1178T>C | p.Leu393Ser | missense_variant | 8/8 | 1 | NM_020395.4 | P1 | |
INTS12 | ENST00000451321.6 | c.1178T>C | p.Leu393Ser | missense_variant | 7/7 | 1 | P1 | ||
INTS12 | ENST00000394735.5 | c.1178T>C | p.Leu393Ser | missense_variant | 8/8 | 5 | P1 | ||
ARHGEF38 | ENST00000503289.1 | n.330A>G | non_coding_transcript_exon_variant | 4/5 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152172Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000796 AC: 2AN: 251412Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135874
GnomAD4 exome AF: 0.00000479 AC: 7AN: 1461828Hom.: 0 Cov.: 31 AF XY: 0.00000688 AC XY: 5AN XY: 727210
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152172Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74348
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 01, 2024 | The c.1178T>C (p.L393S) alteration is located in exon 8 (coding exon 6) of the INTS12 gene. This alteration results from a T to C substitution at nucleotide position 1178, causing the leucine (L) at amino acid position 393 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