chr16-21643152-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_005849.4(IGSF6):āc.588G>Cā(p.Lys196Asn) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000749 in 1,601,910 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_005849.4 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IGSF6 | NM_005849.4 | c.588G>C | p.Lys196Asn | missense_variant, splice_region_variant | 5/6 | ENST00000268389.6 | |
METTL9 | NM_016025.5 | c.752-12075C>G | intron_variant | ENST00000358154.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IGSF6 | ENST00000268389.6 | c.588G>C | p.Lys196Asn | missense_variant, splice_region_variant | 5/6 | 1 | NM_005849.4 | P1 | |
METTL9 | ENST00000358154.8 | c.752-12075C>G | intron_variant | 1 | NM_016025.5 | P3 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 151964Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000404 AC: 1AN: 247362Hom.: 0 AF XY: 0.00000745 AC XY: 1AN XY: 134188
GnomAD4 exome AF: 0.00000552 AC: 8AN: 1449828Hom.: 0 Cov.: 28 AF XY: 0.00000554 AC XY: 4AN XY: 721926
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152082Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74356
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 03, 2024 | The c.588G>C (p.K196N) alteration is located in exon 5 (coding exon 5) of the IGSF6 gene. This alteration results from a G to C substitution at nucleotide position 588, causing the lysine (K) at amino acid position 196 to be replaced by an asparagine (N). 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