13-95194891-G-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_005845.5(ABCC4):c.1208C>T(p.Pro403Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000502 in 1,614,054 control chromosomes in the GnomAD database, including 2 homozygotes. 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 Likely benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_005845.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ABCC4 | NM_005845.5 | c.1208C>T | p.Pro403Leu | missense_variant | 9/31 | ENST00000645237.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ABCC4 | ENST00000645237.2 | c.1208C>T | p.Pro403Leu | missense_variant | 9/31 | NM_005845.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00151 AC: 229AN: 152118Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000505 AC: 127AN: 251398Hom.: 0 AF XY: 0.000397 AC XY: 54AN XY: 135866
GnomAD4 exome AF: 0.000397 AC: 581AN: 1461818Hom.: 1 Cov.: 31 AF XY: 0.000392 AC XY: 285AN XY: 727218
GnomAD4 genome AF: 0.00150 AC: 229AN: 152236Hom.: 1 Cov.: 32 AF XY: 0.00145 AC XY: 108AN XY: 74418
ClinVar
Submissions by phenotype
ABCC4-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | May 22, 2023 | This variant is classified as likely 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