rs193920904
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_001089.3(ABCA3):c.2086G>A(p.Asp696Asn) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,461,006 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 12/21 in silico tools predict a damaging outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (no stars). Synonymous variant affecting the same amino acid position (i.e. D696D) has been classified as Likely benign.
Frequency
Consequence
NM_001089.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ABCA3 | NM_001089.3 | c.2086G>A | p.Asp696Asn | missense_variant | 17/33 | ENST00000301732.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ABCA3 | ENST00000301732.10 | c.2086G>A | p.Asp696Asn | missense_variant | 17/33 | 1 | NM_001089.3 | P1 | |
ABCA3 | ENST00000382381.7 | c.1912G>A | p.Asp638Asn | missense_variant | 16/32 | 1 | |||
ABCA3 | ENST00000563623.5 | n.2649G>A | non_coding_transcript_exon_variant | 17/20 | 1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461006Hom.: 0 Cov.: 32 AF XY: 0.00000275 AC XY: 2AN XY: 726834
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Malignant tumor of prostate Uncertain:1
Uncertain significance, no assertion criteria provided | literature only | Science for Life laboratory, Karolinska Institutet | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at