16-21643585-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_005849.4(IGSF6):c.548C>T(p.Pro183Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000305 in 1,606,734 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_005849.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IGSF6 | NM_005849.4 | c.548C>T | p.Pro183Leu | missense_variant | 4/6 | ENST00000268389.6 | |
METTL9 | NM_016025.5 | c.752-11642G>A | intron_variant | ENST00000358154.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IGSF6 | ENST00000268389.6 | c.548C>T | p.Pro183Leu | missense_variant | 4/6 | 1 | NM_005849.4 | P1 | |
METTL9 | ENST00000358154.8 | c.752-11642G>A | intron_variant | 1 | NM_016025.5 | P3 |
Frequencies
GnomAD3 genomes AF: 0.000230 AC: 35AN: 152128Hom.: 1 Cov.: 33
GnomAD3 exomes AF: 0.00000802 AC: 2AN: 249280Hom.: 0 AF XY: 0.00000742 AC XY: 1AN XY: 134768
GnomAD4 exome AF: 0.00000962 AC: 14AN: 1454606Hom.: 0 Cov.: 28 AF XY: 0.00000829 AC XY: 6AN XY: 724048
GnomAD4 genome AF: 0.000230 AC: 35AN: 152128Hom.: 1 Cov.: 33 AF XY: 0.000229 AC XY: 17AN XY: 74310
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 17, 2023 | The c.548C>T (p.P183L) alteration is located in exon 4 (coding exon 4) of the IGSF6 gene. This alteration results from a C to T substitution at nucleotide position 548, causing the proline (P) at amino acid position 183 to be replaced by a leucine (L). 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