17-45816483-G-A
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_001303020.2(CRHR1):c.-76G>A variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000235 in 1,613,962 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001303020.2 5_prime_UTR_premature_start_codon_gain
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LINC02210-CRHR1 | ENST00000634540 | c.-384G>A | 5_prime_UTR_premature_start_codon_gain_variant | Exon 5 of 15 | 2 | ENSP00000488912.1 | ||||
CRHR1 | ENST00000314537.10 | c.142G>A | p.Val48Met | missense_variant | Exon 3 of 13 | 1 | NM_004382.5 | ENSP00000326060.6 | ||
LINC02210-CRHR1 | ENST00000634540 | c.-384G>A | 5_prime_UTR_variant | Exon 5 of 15 | 2 | ENSP00000488912.1 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152180Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000401 AC: 1AN: 249304Hom.: 0 AF XY: 0.00000739 AC XY: 1AN XY: 135316
GnomAD4 exome AF: 0.0000239 AC: 35AN: 1461782Hom.: 0 Cov.: 32 AF XY: 0.0000275 AC XY: 20AN XY: 727206
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152180Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74330
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.142G>A (p.V48M) alteration is located in exon 3 (coding exon 3) of the CRHR1 gene. This alteration results from a G to A substitution at nucleotide position 142, causing the valine (V) at amino acid position 48 to be replaced by a methionine (M). 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