chr4-103589412-A-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_001059.3(TACR3):c.*270T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00591 in 396,916 control chromosomes in the GnomAD database, including 48 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.012 ( 38 hom., cov: 33)
Exomes 𝑓: 0.0019 ( 10 hom. )
Consequence
TACR3
NM_001059.3 3_prime_UTR
NM_001059.3 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0250
Genes affected
TACR3 (HGNC:11528): (tachykinin receptor 3) This gene belongs to a family of genes that function as receptors for tachykinins. Receptor affinities are specified by variations in the 5'-end of the sequence. The receptors belonging to this family are characterized by interactions with G proteins and 7 hydrophobic transmembrane regions. This gene encodes the receptor for the tachykinin neurokinin 3, also referred to as neurokinin B. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BP6
?
Variant 4-103589412-A-G is Benign according to our data. Variant chr4-103589412-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 1204446.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0124 (1887/152248) while in subpopulation AFR AF= 0.0434 (1805/41564). AF 95% confidence interval is 0.0418. There are 38 homozygotes in gnomad4. There are 895 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 38 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TACR3 | NM_001059.3 | c.*270T>C | 3_prime_UTR_variant | 5/5 | ENST00000304883.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TACR3 | ENST00000304883.3 | c.*270T>C | 3_prime_UTR_variant | 5/5 | 1 | NM_001059.3 | P1 | ||
TACR3-AS1 | ENST00000502936.1 | n.190-1795A>G | intron_variant, non_coding_transcript_variant | 2 | |||||
TACR3-AS1 | ENST00000512401.5 | n.292-1795A>G | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0124 AC: 1883AN: 152130Hom.: 38 Cov.: 33
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GnomAD4 exome AF: 0.00187 AC: 457AN: 244668Hom.: 10 Cov.: 2 AF XY: 0.00154 AC XY: 196AN XY: 127318
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GnomAD4 genome ? AF: 0.0124 AC: 1887AN: 152248Hom.: 38 Cov.: 33 AF XY: 0.0120 AC XY: 895AN XY: 74446
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | May 10, 2019 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at