17-44967711-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_006688.5(C1QL1):c.338C>T(p.Ala113Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000323 in 1,609,824 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_006688.5 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 |
---|---|---|---|---|---|---|---|---|
C1QL1 | NM_006688.5 | c.338C>T | p.Ala113Val | missense_variant | 1/2 | ENST00000253407.4 | NP_006679.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
C1QL1 | ENST00000253407.4 | c.338C>T | p.Ala113Val | missense_variant | 1/2 | 1 | NM_006688.5 | ENSP00000253407 | P1 | |
NMT1 | ENST00000678938.1 | c.-110+9649G>A | intron_variant | ENSP00000503621 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152030Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000920 AC: 22AN: 239136Hom.: 0 AF XY: 0.0000992 AC XY: 13AN XY: 131022
GnomAD4 exome AF: 0.0000309 AC: 45AN: 1457676Hom.: 0 Cov.: 32 AF XY: 0.0000317 AC XY: 23AN XY: 725140
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152148Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74384
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 31, 2023 | The c.338C>T (p.A113V) alteration is located in exon 1 (coding exon 1) of the C1QL1 gene. This alteration results from a C to T substitution at nucleotide position 338, causing the alanine (A) at amino acid position 113 to be replaced by a valine (V). 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