9-4679871-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_017913.4(CDC37L1):c.104G>A(p.Cys35Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000533 in 1,613,894 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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_017913.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CDC37L1 | ENST00000381854.4 | c.104G>A | p.Cys35Tyr | missense_variant | Exon 1 of 7 | 1 | NM_017913.4 | ENSP00000371278.3 | ||
CDC37L1 | ENST00000381858.5 | c.104G>A | p.Cys35Tyr | missense_variant | Exon 1 of 7 | 5 | ENSP00000371282.1 | |||
CDC37L1 | ENST00000479095.1 | n.157G>A | non_coding_transcript_exon_variant | Exon 1 of 2 | 2 |
Frequencies
GnomAD3 genomes AF: 0.000335 AC: 51AN: 152244Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000605 AC: 15AN: 248080Hom.: 0 AF XY: 0.0000371 AC XY: 5AN XY: 134728
GnomAD4 exome AF: 0.0000239 AC: 35AN: 1461532Hom.: 0 Cov.: 30 AF XY: 0.0000179 AC XY: 13AN XY: 727092
GnomAD4 genome AF: 0.000335 AC: 51AN: 152362Hom.: 0 Cov.: 33 AF XY: 0.000376 AC XY: 28AN XY: 74502
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.104G>A (p.C35Y) alteration is located in exon 2 (coding exon 1) of the CDC37L1 gene. This alteration results from a G to A substitution at nucleotide position 104, causing the cysteine (C) at amino acid position 35 to be replaced by a tyrosine (Y). 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