3-184036084-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001145143.1(HTR3D):c.181G>A(p.Val61Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00143 in 1,551,436 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001145143.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HTR3D | NM_001145143.1 | c.181G>A | p.Val61Ile | missense_variant | 3/8 | ENST00000428798.7 | NP_001138615.1 | |
HTR3D | NM_001163646.2 | c.364G>A | p.Val122Ile | missense_variant | 3/8 | NP_001157118.1 | ||
HTR3D | NM_182537.3 | c.-31-285G>A | intron_variant | NP_872343.2 | ||||
HTR3D | NM_001410851.1 | c.3+862G>A | intron_variant | NP_001397780.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HTR3D | ENST00000428798.7 | c.181G>A | p.Val61Ile | missense_variant | 3/8 | 5 | NM_001145143.1 | ENSP00000405409.2 | ||
HTR3D | ENST00000382489.3 | c.364G>A | p.Val122Ile | missense_variant | 3/8 | 1 | ENSP00000371929.3 | |||
HTR3D | ENST00000334128.6 | c.-31-285G>A | intron_variant | 1 | ENSP00000334315.2 | |||||
HTR3D | ENST00000453435.1 | c.3+862G>A | intron_variant | 1 | ENSP00000389268.1 |
Frequencies
GnomAD3 genomes AF: 0.000973 AC: 148AN: 152184Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000824 AC: 129AN: 156468Hom.: 0 AF XY: 0.000785 AC XY: 65AN XY: 82854
GnomAD4 exome AF: 0.00149 AC: 2078AN: 1399134Hom.: 1 Cov.: 32 AF XY: 0.00146 AC XY: 1008AN XY: 690100
GnomAD4 genome AF: 0.000972 AC: 148AN: 152302Hom.: 0 Cov.: 32 AF XY: 0.000900 AC XY: 67AN XY: 74476
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 30, 2021 | 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