5-168669872-T-C
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_003062.4(SLIT3):āc.4247A>Gā(p.Lys1416Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000675 in 1,614,076 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/23 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_003062.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLIT3 | NM_003062.4 | c.4247A>G | p.Lys1416Arg | missense_variant | 35/36 | ENST00000519560.6 | NP_003053.2 | |
SLIT3 | NM_001271946.2 | c.4268A>G | p.Lys1423Arg | missense_variant | 35/36 | NP_001258875.2 | ||
SLIT3 | XM_017009779.1 | c.4058A>G | p.Lys1353Arg | missense_variant | 35/36 | XP_016865268.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLIT3 | ENST00000519560.6 | c.4247A>G | p.Lys1416Arg | missense_variant | 35/36 | 1 | NM_003062.4 | ENSP00000430333 | A1 | |
SLIT3 | ENST00000332966.8 | c.4268A>G | p.Lys1423Arg | missense_variant | 35/36 | 1 | ENSP00000332164 | P4 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152204Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000107 AC: 27AN: 251458Hom.: 1 AF XY: 0.000147 AC XY: 20AN XY: 135900
GnomAD4 exome AF: 0.0000739 AC: 108AN: 1461872Hom.: 2 Cov.: 32 AF XY: 0.000107 AC XY: 78AN XY: 727230
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152204Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74356
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 14, 2023 | The c.4247A>G (p.K1416R) alteration is located in exon 35 (coding exon 35) of the SLIT3 gene. This alteration results from a A to G substitution at nucleotide position 4247, causing the lysine (K) at amino acid position 1416 to be replaced by an arginine (R). 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