chr2-43813181-T-A
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_022436.3(ABCG5):c.1891A>T(p.Ile631Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000193 in 1,558,064 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 (★).
Frequency
Consequence
NM_022436.3 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 | UniProt |
---|---|---|---|---|---|---|---|
ABCG5 | NM_022436.3 | c.1891A>T | p.Ile631Phe | missense_variant | 13/13 | ENST00000405322.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ABCG5 | ENST00000405322.8 | c.1891A>T | p.Ile631Phe | missense_variant | 13/13 | 1 | NM_022436.3 | P1 | |
ABCG5 | ENST00000486512.5 | n.2412A>T | non_coding_transcript_exon_variant | 9/9 | 1 | ||||
ABCG5 | ENST00000409962.1 | n.2174A>T | non_coding_transcript_exon_variant | 9/9 | 2 | ||||
ABCG5 | ENST00000644754.1 | n.2275A>T | non_coding_transcript_exon_variant | 10/10 |
Frequencies
GnomAD3 genomes ? AF: 0.000131 AC: 20AN: 152256Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 250662Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135464
GnomAD4 exome AF: 0.00000711 AC: 10AN: 1405808Hom.: 0 Cov.: 25 AF XY: 0.0000128 AC XY: 9AN XY: 703110
GnomAD4 genome ? AF: 0.000131 AC: 20AN: 152256Hom.: 0 Cov.: 32 AF XY: 0.000188 AC XY: 14AN XY: 74392
ClinVar
Submissions by phenotype
Cardiovascular phenotype Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 26, 2023 | The p.I631F variant (also known as c.1891A>T), located in coding exon 13 of the ABCG5 gene, results from an A to T substitution at nucleotide position 1891. The isoleucine at codon 631 is replaced by phenylalanine, an amino acid with highly similar properties. This amino acid position is conserved. In addition, the in silico prediction for this alteration is inconclusive. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at