NM_001217.5:c.22A>G
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001217.5(CA11):c.22A>G(p.Ser8Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000282 in 1,598,458 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001217.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CA11 | NM_001217.5 | c.22A>G | p.Ser8Gly | missense_variant | Exon 1 of 9 | ENST00000084798.9 | NP_001208.2 | |
CA11 | NR_136241.2 | n.577A>G | non_coding_transcript_exon_variant | Exon 1 of 9 | ||||
SEC1P | NR_004401.2 | n.108+7465T>C | intron_variant | Intron 1 of 4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CA11 | ENST00000084798.9 | c.22A>G | p.Ser8Gly | missense_variant | Exon 1 of 9 | 1 | NM_001217.5 | ENSP00000084798.3 | ||
SEC1P | ENST00000474419.5 | n.76+7465T>C | intron_variant | Intron 1 of 3 | 1 | |||||
SEC1P | ENST00000483163.1 | n.76+7465T>C | intron_variant | Intron 1 of 1 | 1 | |||||
SEC1P | ENST00000430145.3 | n.48+7465T>C | intron_variant | Intron 1 of 4 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000595 AC: 9AN: 151328Hom.: 0 Cov.: 31
GnomAD4 exome AF: 0.0000249 AC: 36AN: 1447130Hom.: 0 Cov.: 33 AF XY: 0.0000167 AC XY: 12AN XY: 718574
GnomAD4 genome AF: 0.0000595 AC: 9AN: 151328Hom.: 0 Cov.: 31 AF XY: 0.0000541 AC XY: 4AN XY: 73920
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.22A>G (p.S8G) alteration is located in exon 1 (coding exon 1) of the CA11 gene. This alteration results from a A to G substitution at nucleotide position 22, causing the serine (S) at amino acid position 8 to be replaced by a glycine (G). 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