rs138475920
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_ModerateBP6_ModerateBP7
The NM_000350.3(ABCA4):c.4611G>C(p.Thr1537=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000018 in 1,614,016 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. T1537T) has been classified as Likely benign.
Frequency
Consequence
NM_000350.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ABCA4 | NM_000350.3 | c.4611G>C | p.Thr1537= | synonymous_variant | 31/50 | ENST00000370225.4 | |
ABCA4 | XM_047416704.1 | c.4389G>C | p.Thr1463= | synonymous_variant | 30/49 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ABCA4 | ENST00000370225.4 | c.4611G>C | p.Thr1537= | synonymous_variant | 31/50 | 1 | NM_000350.3 | P1 | |
ABCA4 | ENST00000460514.1 | n.105G>C | non_coding_transcript_exon_variant | 2/7 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.000112 AC: 17AN: 152200Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000398 AC: 10AN: 251474Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135908
GnomAD4 exome AF: 0.00000821 AC: 12AN: 1461816Hom.: 0 Cov.: 31 AF XY: 0.00000413 AC XY: 3AN XY: 727220
GnomAD4 genome ? AF: 0.000112 AC: 17AN: 152200Hom.: 0 Cov.: 33 AF XY: 0.000134 AC XY: 10AN XY: 74352
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 21, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at