chr1-23193426-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_000864.5(HTR1D):c.794C>T(p.Ser265Leu) variant causes a missense change. The variant allele was found at a frequency of 0.0015 in 1,614,208 control chromosomes in the GnomAD database, including 37 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_000864.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HTR1D | NM_000864.5 | c.794C>T | p.Ser265Leu | missense_variant | 2/2 | ENST00000374619.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HTR1D | ENST00000374619.2 | c.794C>T | p.Ser265Leu | missense_variant | 2/2 | NM_000864.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00795 AC: 1210AN: 152212Hom.: 26 Cov.: 32
GnomAD3 exomes AF: 0.00209 AC: 526AN: 251422Hom.: 3 AF XY: 0.00154 AC XY: 209AN XY: 135894
GnomAD4 exome AF: 0.000829 AC: 1212AN: 1461878Hom.: 11 Cov.: 33 AF XY: 0.000689 AC XY: 501AN XY: 727238
GnomAD4 genome ? AF: 0.00796 AC: 1212AN: 152330Hom.: 26 Cov.: 32 AF XY: 0.00785 AC XY: 585AN XY: 74498
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | May 22, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at