chr1-6575249-C-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_138697.4(TAS1R1):c.1117C>A(p.His373Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00137 in 1,613,486 control chromosomes in the GnomAD database, including 27 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 Benign (★).
Frequency
Consequence
NM_138697.4 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 |
---|---|---|---|---|---|---|---|
TAS1R1 | NM_138697.4 | c.1117C>A | p.His373Asn | missense_variant | 3/6 | ENST00000333172.11 | |
LOC107984912 | XR_002958250.1 | n.87+4098G>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TAS1R1 | ENST00000333172.11 | c.1117C>A | p.His373Asn | missense_variant | 3/6 | 1 | NM_138697.4 | P1 | |
TAS1R1 | ENST00000415267.1 | c.276-1166C>A | intron_variant | 1 | |||||
TAS1R1 | ENST00000411823.5 | c.895C>A | p.His299Asn | missense_variant | 2/3 | 2 | |||
TAS1R1 | ENST00000351136.7 | c.499-1166C>A | intron_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00710 AC: 1081AN: 152250Hom.: 11 Cov.: 32
GnomAD3 exomes AF: 0.00217 AC: 543AN: 249916Hom.: 12 AF XY: 0.00165 AC XY: 224AN XY: 135466
GnomAD4 exome AF: 0.000775 AC: 1132AN: 1461118Hom.: 17 Cov.: 34 AF XY: 0.000649 AC XY: 472AN XY: 726872
GnomAD4 genome ? AF: 0.00711 AC: 1083AN: 152368Hom.: 10 Cov.: 32 AF XY: 0.00652 AC XY: 486AN XY: 74510
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | May 31, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at