19-48639563-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_001217.5(CA11):c.626G>A(p.Arg209His) variant causes a missense change. The variant allele was found at a frequency of 0.0000806 in 1,613,800 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CA11 | NM_001217.5 | c.626G>A | p.Arg209His | missense_variant | Exon 6 of 9 | ENST00000084798.9 | NP_001208.2 | |
CA11 | NR_136241.2 | n.1181G>A | non_coding_transcript_exon_variant | Exon 6 of 9 | ||||
SEC1P | NR_004401.2 | n.108+1417C>T | intron_variant | Intron 1 of 4 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000461 AC: 7AN: 151966Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000278 AC: 7AN: 251414Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135876
GnomAD4 exome AF: 0.0000841 AC: 123AN: 1461834Hom.: 0 Cov.: 32 AF XY: 0.0000839 AC XY: 61AN XY: 727220
GnomAD4 genome AF: 0.0000461 AC: 7AN: 151966Hom.: 0 Cov.: 31 AF XY: 0.0000539 AC XY: 4AN XY: 74218
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.626G>A (p.R209H) alteration is located in exon 6 (coding exon 6) of the CA11 gene. This alteration results from a G to A substitution at nucleotide position 626, causing the arginine (R) at amino acid position 209 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