rs375249271
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_000863.3(HTR1B):āc.518T>Cā(p.Val173Ala) variant causes a missense change. The variant allele was found at a frequency of 0.00000744 in 1,613,882 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 (ā ).
Frequency
Consequence
NM_000863.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HTR1B | NM_000863.3 | c.518T>C | p.Val173Ala | missense_variant | Exon 1 of 1 | ENST00000369947.5 | NP_000854.1 | |
LOC105377864 | XM_047419659.1 | c.-11573A>G | 5_prime_UTR_variant | Exon 2 of 6 | XP_047275615.1 | |||
LOC105377864 | XM_047419660.1 | c.-3742-11640A>G | intron_variant | Intron 5 of 8 | XP_047275616.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000591 AC: 9AN: 152192Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000796 AC: 2AN: 251296Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135870
GnomAD4 exome AF: 0.00000205 AC: 3AN: 1461690Hom.: 0 Cov.: 38 AF XY: 0.00000138 AC XY: 1AN XY: 727134
GnomAD4 genome AF: 0.0000591 AC: 9AN: 152192Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74352
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.518T>C (p.V173A) alteration is located in exon 1 (coding exon 1) of the HTR1B gene. This alteration results from a T to C substitution at nucleotide position 518, causing the valine (V) at amino acid position 173 to be replaced by an alanine (A). 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