16-3606516-T-C
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_032444.4(SLX4):āc.718A>Gā(p.Asn240Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000774 in 1,614,182 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ).
Frequency
Consequence
NM_032444.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLX4 | NM_032444.4 | c.718A>G | p.Asn240Asp | missense_variant | Exon 3 of 15 | ENST00000294008.4 | NP_115820.2 | |
SLX4 | XM_024450471.2 | c.718A>G | p.Asn240Asp | missense_variant | Exon 3 of 15 | XP_024306239.1 | ||
SLX4 | XM_011522715.4 | c.718A>G | p.Asn240Asp | missense_variant | Exon 3 of 15 | XP_011521017.1 | ||
SLX4 | XR_007064923.1 | n.1367A>G | non_coding_transcript_exon_variant | Exon 3 of 13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLX4 | ENST00000294008.4 | c.718A>G | p.Asn240Asp | missense_variant | Exon 3 of 15 | 5 | NM_032444.4 | ENSP00000294008.3 | ||
SLX4 | ENST00000466154.5 | n.1013A>G | non_coding_transcript_exon_variant | Exon 2 of 7 | 1 | |||||
SLX4 | ENST00000486524.1 | n.1346A>G | non_coding_transcript_exon_variant | Exon 3 of 4 | 2 | |||||
SLX4 | ENST00000697858.1 | n.59A>G | non_coding_transcript_exon_variant | Exon 1 of 3 |
Frequencies
GnomAD3 genomes AF: 0.00438 AC: 667AN: 152178Hom.: 3 Cov.: 32
GnomAD3 exomes AF: 0.00118 AC: 296AN: 250942Hom.: 2 AF XY: 0.000921 AC XY: 125AN XY: 135666
GnomAD4 exome AF: 0.000399 AC: 583AN: 1461888Hom.: 4 Cov.: 32 AF XY: 0.000360 AC XY: 262AN XY: 727246
GnomAD4 genome AF: 0.00438 AC: 667AN: 152294Hom.: 3 Cov.: 32 AF XY: 0.00424 AC XY: 316AN XY: 74474
ClinVar
Submissions by phenotype
not provided Benign:3
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Fanconi anemia complementation group P Benign:2
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not specified Benign:1
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Fanconi anemia Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at