chrX-120366604-T-C
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001142447.3(ATP1B4):c.143T>C(p.Val48Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0108 in 1,200,479 control chromosomes in the GnomAD database, including 644 homozygotes. There are 4,151 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V48M) has been classified as Uncertain significance.
Frequency
Consequence
NM_001142447.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ATP1B4 | NM_001142447.3 | c.143T>C | p.Val48Ala | missense_variant | 2/8 | ENST00000218008.8 | |
ATP1B4 | NM_012069.5 | c.143T>C | p.Val48Ala | missense_variant | 2/8 | ||
ATP1B4 | XM_017029381.2 | c.143T>C | p.Val48Ala | missense_variant | 2/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATP1B4 | ENST00000218008.8 | c.143T>C | p.Val48Ala | missense_variant | 2/8 | 1 | NM_001142447.3 | P1 | |
ATP1B4 | ENST00000361319.3 | c.143T>C | p.Val48Ala | missense_variant | 2/8 | 1 | |||
ATP1B4 | ENST00000539306.5 | c.143T>C | p.Val48Ala | missense_variant | 2/7 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0131 AC: 1435AN: 109647Hom.: 52 Cov.: 22 AF XY: 0.0148 AC XY: 474AN XY: 32009
GnomAD3 exomes AF: 0.0303 AC: 5463AN: 180080Hom.: 243 AF XY: 0.0249 AC XY: 1654AN XY: 66444
GnomAD4 exome AF: 0.0106 AC: 11546AN: 1090779Hom.: 592 Cov.: 29 AF XY: 0.0103 AC XY: 3675AN XY: 356467
GnomAD4 genome ? AF: 0.0131 AC: 1434AN: 109700Hom.: 52 Cov.: 22 AF XY: 0.0148 AC XY: 476AN XY: 32072
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at