3-159764623-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_014575.4(SCHIP1):c.244C>T(p.Pro82Ser) variant causes a missense change. The variant allele was found at a frequency of 0.0000249 in 1,608,392 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_014575.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
IQCJ-SCHIP1 | ENST00000638749.2 | c.244C>T | p.Pro82Ser | missense_variant | Exon 2 of 8 | 1 | NM_014575.4 | ENSP00000491030.1 | ||
IQCJ-SCHIP1 | ENST00000485419.7 | c.472C>T | p.Pro158Ser | missense_variant | Exon 5 of 11 | 2 | ENSP00000420182.1 |
Frequencies
GnomAD3 genomes AF: 0.0000789 AC: 12AN: 152170Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000378 AC: 9AN: 238026Hom.: 0 AF XY: 0.0000311 AC XY: 4AN XY: 128656
GnomAD4 exome AF: 0.0000192 AC: 28AN: 1456104Hom.: 0 Cov.: 31 AF XY: 0.0000111 AC XY: 8AN XY: 723582
GnomAD4 genome AF: 0.0000788 AC: 12AN: 152288Hom.: 0 Cov.: 32 AF XY: 0.000121 AC XY: 9AN XY: 74470
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.472C>T (p.P158S) alteration is located in exon 5 (coding exon 5) of the IQCJ-SCHIP1 gene. This alteration results from a C to T substitution at nucleotide position 472, causing the proline (P) at amino acid position 158 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