chr17-45829614-C-A
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The ENST00000398285.7(CRHR1):c.488C>A(p.Ala163Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000248 in 1,551,054 control chromosomes in the GnomAD database, including 6 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A163S) has been classified as Likely benign.
Frequency
Consequence
ENST00000398285.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CRHR1 | NM_004382.5 | c.434+293C>A | intron_variant | ENST00000314537.10 | |||
LINC02210-CRHR1 | NM_001256299.3 | c.-92+293C>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CRHR1 | ENST00000314537.10 | c.434+293C>A | intron_variant | 1 | NM_004382.5 | P1 | |||
MAPT-AS1 | ENST00000634876.2 | n.604-253G>T | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.000105 AC: 16AN: 152134Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000670 AC: 103AN: 153740Hom.: 2 AF XY: 0.000968 AC XY: 79AN XY: 81640
GnomAD4 exome AF: 0.000264 AC: 369AN: 1398802Hom.: 6 Cov.: 32 AF XY: 0.000378 AC XY: 261AN XY: 689926
GnomAD4 genome AF: 0.000105 AC: 16AN: 152252Hom.: 0 Cov.: 33 AF XY: 0.000202 AC XY: 15AN XY: 74428
ClinVar
Submissions by phenotype
CRHR1-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Dec 28, 2022 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at