chr1-158256900-G-A
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_001763.3(CD1A):c.719G>A(p.Gly240Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00368 in 1,614,210 control chromosomes in the GnomAD database, including 18 homozygotes. 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 Likely benign (★★).
Frequency
Consequence
NM_001763.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CD1A | NM_001763.3 | c.719G>A | p.Gly240Asp | missense_variant | 4/6 | ENST00000289429.6 | |
CD1A | NM_001320652.2 | c.686G>A | p.Gly229Asp | missense_variant | 4/6 | ||
CD1A | XM_024450738.2 | c.251G>A | p.Gly84Asp | missense_variant | 5/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CD1A | ENST00000289429.6 | c.719G>A | p.Gly240Asp | missense_variant | 4/6 | 1 | NM_001763.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00281 AC: 428AN: 152210Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.00284 AC: 714AN: 251492Hom.: 6 AF XY: 0.00288 AC XY: 392AN XY: 135920
GnomAD4 exome AF: 0.00377 AC: 5506AN: 1461882Hom.: 17 Cov.: 33 AF XY: 0.00381 AC XY: 2774AN XY: 727242
GnomAD4 genome AF: 0.00280 AC: 427AN: 152328Hom.: 1 Cov.: 32 AF XY: 0.00266 AC XY: 198AN XY: 74476
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Aug 15, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at