NM_001378511.1:c.62T>A
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The NM_001378511.1(ATP2C1):c.62T>A(p.Ile21Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000288 in 1,424,734 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).
Frequency
Consequence
NM_001378511.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ATP2C1 | NM_001378511.1 | c.62T>A | p.Ile21Asn | missense_variant | Exon 1 of 28 | NP_001365440.1 | ||
ATP2C1 | NM_001199180.2 | c.62T>A | p.Ile21Asn | missense_variant | Exon 1 of 28 | NP_001186109.1 | ||
ATP2C1 | NM_001199181.3 | c.62T>A | p.Ile21Asn | missense_variant | Exon 1 of 27 | NP_001186110.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ATP2C1 | ENST00000507488.6 | c.62T>A | p.Ile21Asn | missense_variant | Exon 1 of 28 | 2 | ENSP00000421326.3 | |||
ATP2C1 | ENST00000505330.5 | c.62T>A | p.Ile21Asn | missense_variant | Exon 1 of 27 | 2 | ENSP00000423774.2 | |||
ATP2C1 | ENST00000504381.5 | c.62T>A | p.Ile21Asn | missense_variant | Exon 1 of 27 | 2 | ENSP00000425320.2 | |||
ATP2C1 | ENST00000509150.1 | n.100T>A | non_coding_transcript_exon_variant | Exon 1 of 3 | 3 |
Frequencies
GnomAD3 genomes AF: 0.00147 AC: 223AN: 152208Hom.: 2 Cov.: 33
GnomAD3 exomes AF: 0.000180 AC: 11AN: 61204Hom.: 0 AF XY: 0.000141 AC XY: 5AN XY: 35470
GnomAD4 exome AF: 0.000149 AC: 189AN: 1272408Hom.: 2 Cov.: 28 AF XY: 0.000141 AC XY: 88AN XY: 624140
GnomAD4 genome AF: 0.00146 AC: 222AN: 152326Hom.: 2 Cov.: 33 AF XY: 0.00134 AC XY: 100AN XY: 74496
ClinVar
Submissions by phenotype
ATP2C1-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at