3-183949871-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 4P and 4B. PP3_StrongBS2
The NM_005688.4(ABCC5):c.3109C>T(p.Arg1037Trp) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000142 in 1,614,076 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 13/21 in silico tools predict a damaging outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_005688.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ABCC5 | ENST00000334444.11 | c.3109C>T | p.Arg1037Trp | missense_variant | 22/30 | 1 | NM_005688.4 | ENSP00000333926.6 | ||
ABCC5 | ENST00000265586.10 | c.3098+101C>T | intron_variant | 5 | ENSP00000265586.6 | |||||
ABCC5 | ENST00000437205.5 | n.*1802C>T | non_coding_transcript_exon_variant | 22/30 | 5 | ENSP00000403510.1 | ||||
ABCC5 | ENST00000437205.5 | n.*1802C>T | 3_prime_UTR_variant | 22/30 | 5 | ENSP00000403510.1 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152198Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000200 AC: 5AN: 249452Hom.: 0 AF XY: 0.0000222 AC XY: 3AN XY: 135336
GnomAD4 exome AF: 0.0000137 AC: 20AN: 1461878Hom.: 0 Cov.: 31 AF XY: 0.0000151 AC XY: 11AN XY: 727236
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152198Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74358
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 25, 2023 | The c.3109C>T (p.R1037W) alteration is located in exon 22 (coding exon 21) of the ABCC5 gene. This alteration results from a C to T substitution at nucleotide position 3109, causing the arginine (R) at amino acid position 1037 to be replaced by a tryptophan (W). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at