chr13-95083230-T-C
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_005845.5(ABCC4):c.2596A>G(p.Ile866Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00489 in 1,614,080 control chromosomes in the GnomAD database, including 35 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as 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 Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ABCC4 | NM_005845.5 | c.2596A>G | p.Ile866Val | missense_variant | 21/31 | ENST00000645237.2 | |
ABCC4 | NM_001301829.2 | c.2455A>G | p.Ile819Val | missense_variant | 20/30 | ||
ABCC4 | XM_047430034.1 | c.2467A>G | p.Ile823Val | missense_variant | 21/31 | ||
ABCC4 | XM_047430035.1 | c.2047A>G | p.Ile683Val | missense_variant | 18/28 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ABCC4 | ENST00000645237.2 | c.2596A>G | p.Ile866Val | missense_variant | 21/31 | NM_005845.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00370 AC: 563AN: 152162Hom.: 5 Cov.: 32
GnomAD3 exomes AF: 0.00410 AC: 1031AN: 251180Hom.: 7 AF XY: 0.00424 AC XY: 575AN XY: 135744
GnomAD4 exome AF: 0.00501 AC: 7327AN: 1461800Hom.: 30 Cov.: 31 AF XY: 0.00492 AC XY: 3575AN XY: 727200
GnomAD4 genome ? AF: 0.00370 AC: 563AN: 152280Hom.: 5 Cov.: 32 AF XY: 0.00347 AC XY: 258AN XY: 74458
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jul 20, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at