7-7969363-T-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The ENST00000223145.10(GLCCI1):āc.13T>Gā(p.Ser5Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000159 in 1,321,204 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
ENST00000223145.10 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GLCCI1 | NM_138426.4 | c.13T>G | p.Ser5Ala | missense_variant | 1/8 | ENST00000223145.10 | NP_612435.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GLCCI1 | ENST00000223145.10 | c.13T>G | p.Ser5Ala | missense_variant | 1/8 | 1 | NM_138426.4 | ENSP00000223145 | P1 | |
GLCCI1-DT | ENST00000428660.1 | n.132+409A>C | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes AF: 0.00000669 AC: 1AN: 149546Hom.: 0 Cov.: 30
GnomAD3 exomes AF: 0.0000690 AC: 8AN: 115934Hom.: 0 AF XY: 0.0000908 AC XY: 6AN XY: 66102
GnomAD4 exome AF: 0.0000171 AC: 20AN: 1171658Hom.: 0 Cov.: 31 AF XY: 0.0000259 AC XY: 15AN XY: 579276
GnomAD4 genome AF: 0.00000669 AC: 1AN: 149546Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 72924
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 17, 2023 | The c.13T>G (p.S5A) alteration is located in exon 1 (coding exon 1) of the GLCCI1 gene. This alteration results from a T to G substitution at nucleotide position 13, causing the serine (S) at amino acid position 5 to be replaced by an alanine (A). 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