chr16-21643138-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_005849.4(IGSF6):c.602G>A(p.Arg201His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000651 in 1,605,968 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/21 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.602G>A | p.Arg201His | missense_variant | 5/6 | ENST00000268389.6 | |
METTL9 | NM_016025.5 | c.752-12089C>T | intron_variant | ENST00000358154.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IGSF6 | ENST00000268389.6 | c.602G>A | p.Arg201His | missense_variant | 5/6 | 1 | NM_005849.4 | P1 | |
METTL9 | ENST00000358154.8 | c.752-12089C>T | intron_variant | 1 | NM_016025.5 | P3 |
Frequencies
GnomAD3 genomes AF: 0.000553 AC: 84AN: 151796Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000600 AC: 149AN: 248506Hom.: 0 AF XY: 0.000654 AC XY: 88AN XY: 134598
GnomAD4 exome AF: 0.000661 AC: 961AN: 1454054Hom.: 1 Cov.: 29 AF XY: 0.000670 AC XY: 485AN XY: 723808
GnomAD4 genome AF: 0.000553 AC: 84AN: 151914Hom.: 0 Cov.: 33 AF XY: 0.000606 AC XY: 45AN XY: 74258
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 09, 2022 | The c.602G>A (p.R201H) alteration is located in exon 5 (coding exon 5) of the IGSF6 gene. This alteration results from a G to A substitution at nucleotide position 602, causing the arginine (R) at amino acid position 201 to be replaced by a histidine (H). 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