19-1783197-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_138813.4(ATP8B3):āc.3734C>Gā(p.Ser1245Cys) variant causes a missense change. The variant allele was found at a frequency of 0.000000685 in 1,460,774 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_138813.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ATP8B3 | NM_138813.4 | c.3734C>G | p.Ser1245Cys | missense_variant | 29/29 | ENST00000310127.10 | NP_620168.1 | |
ATP8B3 | NM_001178002.3 | c.3623C>G | p.Ser1208Cys | missense_variant | 29/29 | NP_001171473.1 | ||
ATP8B3 | NR_047593.3 | n.4117C>G | non_coding_transcript_exon_variant | 29/29 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ATP8B3 | ENST00000310127.10 | c.3734C>G | p.Ser1245Cys | missense_variant | 29/29 | 1 | NM_138813.4 | ENSP00000311336.6 | ||
ATP8B3 | ENST00000525591.5 | c.3623C>G | p.Ser1208Cys | missense_variant | 29/29 | 1 | ENSP00000437115.1 | |||
ATP8B3 | ENST00000531925.5 | n.*3617C>G | non_coding_transcript_exon_variant | 29/29 | 2 | ENSP00000444334.1 | ||||
ATP8B3 | ENST00000531925.5 | n.*3617C>G | 3_prime_UTR_variant | 29/29 | 2 | ENSP00000444334.1 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD4 exome AF: 6.85e-7 AC: 1AN: 1460774Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 726564
GnomAD4 genome Cov.: 31
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 12, 2022 | The c.3734C>G (p.S1245C) alteration is located in exon 29 (coding exon 28) of the ATP8B3 gene. This alteration results from a C to G substitution at nucleotide position 3734, causing the serine (S) at amino acid position 1245 to be replaced by a cysteine (C). 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
Publications
No publications associated with this variant yet.