chr1-152515441-G-A
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_019060.3(CRCT1):c.58G>A(p.Gly20Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00979 in 1,598,488 control chromosomes in the GnomAD database, including 1,007 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/18 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_019060.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CRCT1 | NM_019060.3 | c.58G>A | p.Gly20Ser | missense_variant | 2/2 | ENST00000368790.4 | |
CRCT1 | XM_011509656.3 | c.58G>A | p.Gly20Ser | missense_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CRCT1 | ENST00000368790.4 | c.58G>A | p.Gly20Ser | missense_variant | 2/2 | 1 | NM_019060.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0464 AC: 7065AN: 152172Hom.: 510 Cov.: 32
GnomAD3 exomes AF: 0.0130 AC: 2990AN: 229668Hom.: 203 AF XY: 0.00997 AC XY: 1257AN XY: 126088
GnomAD4 exome AF: 0.00592 AC: 8567AN: 1446198Hom.: 495 Cov.: 32 AF XY: 0.00540 AC XY: 3879AN XY: 718690
GnomAD4 genome AF: 0.0465 AC: 7075AN: 152290Hom.: 512 Cov.: 32 AF XY: 0.0442 AC XY: 3290AN XY: 74468
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at