3-183942813-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 1P and 7B. PP2BP4BP6_ModerateBS2
The NM_005688.4(ABCC5):c.3608G>A(p.Arg1203Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000502 in 1,614,024 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 Likely benign (★).
Frequency
Consequence
NM_005688.4 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 |
---|---|---|---|---|---|---|---|
ABCC5 | NM_005688.4 | c.3608G>A | p.Arg1203Gln | missense_variant | 25/30 | ENST00000334444.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ABCC5 | ENST00000334444.11 | c.3608G>A | p.Arg1203Gln | missense_variant | 25/30 | 1 | NM_005688.4 | P1 | |
ABCC5 | ENST00000265586.10 | c.3479G>A | p.Arg1160Gln | missense_variant | 24/29 | 5 | |||
ABCC5 | ENST00000437205.5 | c.*2301G>A | 3_prime_UTR_variant, NMD_transcript_variant | 25/30 | 5 | ||||
ABCC5 | ENST00000443497.1 | upstream_gene_variant | 4 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152142Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000200 AC: 5AN: 249482Hom.: 0 AF XY: 0.0000296 AC XY: 4AN XY: 135358
GnomAD4 exome AF: 0.0000506 AC: 74AN: 1461882Hom.: 0 Cov.: 31 AF XY: 0.0000605 AC XY: 44AN XY: 727244
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152142Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74306
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 04, 2022 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at