17-45830157-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_ModerateBP6_Moderate
The NM_001256299.3(LINC02210-CRHR1):c.-28C>T 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 0.0000285 in 1,614,042 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 Likely benign (★).
Frequency
Consequence
NM_001256299.3 5_prime_UTR_premature_start_codon_gain
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 |
---|---|---|---|---|---|---|---|---|---|---|
LINC02210-CRHR1 | ENST00000634540 | c.-28C>T | 5_prime_UTR_premature_start_codon_gain_variant | Exon 8 of 15 | 2 | ENSP00000488912.1 | ||||
CRHR1 | ENST00000314537.10 | c.498C>T | p.Asn166Asn | synonymous_variant | Exon 6 of 13 | 1 | NM_004382.5 | ENSP00000326060.6 | ||
LINC02210-CRHR1 | ENST00000634540 | c.-28C>T | 5_prime_UTR_variant | Exon 8 of 15 | 2 | ENSP00000488912.1 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152194Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000681 AC: 17AN: 249490Hom.: 0 AF XY: 0.0000813 AC XY: 11AN XY: 135356
GnomAD4 exome AF: 0.0000267 AC: 39AN: 1461848Hom.: 0 Cov.: 32 AF XY: 0.0000303 AC XY: 22AN XY: 727230
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152194Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74338
ClinVar
Submissions by phenotype
not specified Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at