7-143478284-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_176883.2(TAS2R41):c.412G>A(p.Val138Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000558 in 1,613,892 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V138D) has been classified as Uncertain significance.
Frequency
Consequence
NM_176883.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TAS2R41 | NM_176883.2 | c.412G>A | p.Val138Ile | missense_variant | 1/1 | ENST00000408916.1 | |
EPHA1-AS1 | NR_033897.1 | n.207-26490G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TAS2R41 | ENST00000408916.1 | c.412G>A | p.Val138Ile | missense_variant | 1/1 | NM_176883.2 | P1 | ||
EPHA1-AS1 | ENST00000429289.5 | n.207-26490G>A | intron_variant, non_coding_transcript_variant | 1 | |||||
EPHA1-AS1 | ENST00000690912.1 | n.228-17682G>A | intron_variant, non_coding_transcript_variant | ||||||
EPHA1-AS1 | ENST00000703017.1 | n.206-17682G>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.0000395 AC: 6AN: 152022Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 249166Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135174
GnomAD4 exome AF: 0.00000205 AC: 3AN: 1461870Hom.: 0 Cov.: 34 AF XY: 0.00 AC XY: 0AN XY: 727238
GnomAD4 genome ? AF: 0.0000395 AC: 6AN: 152022Hom.: 0 Cov.: 31 AF XY: 0.0000269 AC XY: 2AN XY: 74258
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 10, 2022 | The c.412G>A (p.V138I) alteration is located in exon 1 (coding exon 1) of the TAS2R41 gene. This alteration results from a G to A substitution at nucleotide position 412, causing the valine (V) at amino acid position 138 to be replaced by an isoleucine (I). 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