8-74244568-G-C
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_020647.4(JPH1):āc.1866C>Gā(p.Ser622Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000304 in 1,612,896 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_020647.4 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 |
---|---|---|---|---|---|---|---|
JPH1 | NM_020647.4 | c.1866C>G | p.Ser622Arg | missense_variant | 4/6 | ENST00000342232.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
JPH1 | ENST00000342232.5 | c.1866C>G | p.Ser622Arg | missense_variant | 4/6 | 1 | NM_020647.4 | P1 | |
JPH1 | ENST00000519947.1 | c.*1261C>G | 3_prime_UTR_variant, NMD_transcript_variant | 4/5 | 1 | ||||
JPH1 | ENST00000518195.1 | n.221C>G | non_coding_transcript_exon_variant | 1/3 | 4 |
Frequencies
GnomAD3 genomes AF: 0.000164 AC: 25AN: 152188Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000280 AC: 7AN: 250026Hom.: 0 AF XY: 0.00000740 AC XY: 1AN XY: 135080
GnomAD4 exome AF: 0.0000164 AC: 24AN: 1460590Hom.: 0 Cov.: 32 AF XY: 0.0000124 AC XY: 9AN XY: 726608
GnomAD4 genome AF: 0.000164 AC: 25AN: 152306Hom.: 0 Cov.: 32 AF XY: 0.000188 AC XY: 14AN XY: 74474
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 05, 2023 | The c.1866C>G (p.S622R) alteration is located in exon 4 (coding exon 4) of the JPH1 gene. This alteration results from a C to G substitution at nucleotide position 1866, causing the serine (S) at amino acid position 622 to be replaced by an arginine (R). 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