rs17061412
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BS1BS2
The NM_175067.1(TAAR6):āc.744A>Gā(p.Arg248=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00164 in 1,614,110 control chromosomes in the GnomAD database, including 32 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: š 0.0089 ( 15 hom., cov: 32)
Exomes š: 0.00089 ( 17 hom. )
Consequence
TAAR6
NM_175067.1 synonymous
NM_175067.1 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.37
Genes affected
TAAR6 (HGNC:20978): (trace amine associated receptor 6) This gene encodes a seven-transmembrane G-protein-coupled receptor that likely functions as a receptor for endogenous trace amines. Mutations in this gene may be associated with schizophrenia.[provided by RefSeq, Feb 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.69).
BP7
?
Synonymous conserved (PhyloP=1.37 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00891 (1357/152338) while in subpopulation AFR AF= 0.0303 (1259/41576). AF 95% confidence interval is 0.0289. There are 15 homozygotes in gnomad4. There are 629 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd4 at 15 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TAAR6 | NM_175067.1 | c.744A>G | p.Arg248= | synonymous_variant | 1/1 | ENST00000275198.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TAAR6 | ENST00000275198.1 | c.744A>G | p.Arg248= | synonymous_variant | 1/1 | NM_175067.1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00889 AC: 1353AN: 152220Hom.: 15 Cov.: 32
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GnomAD3 exomes AF: 0.00231 AC: 579AN: 250932Hom.: 3 AF XY: 0.00177 AC XY: 240AN XY: 135640
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GnomAD4 exome AF: 0.000887 AC: 1296AN: 1461772Hom.: 17 Cov.: 32 AF XY: 0.000791 AC XY: 575AN XY: 727196
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GnomAD4 genome ? AF: 0.00891 AC: 1357AN: 152338Hom.: 15 Cov.: 32 AF XY: 0.00844 AC XY: 629AN XY: 74486
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at