3-186671649-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PP3_Moderate
The NM_000412.5(HRG):c.418G>T(p.Asp140Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000013 in 1,613,942 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic 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. D140V) has been classified as Uncertain significance.
Frequency
Consequence
NM_000412.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HRG | NM_000412.5 | c.418G>T | p.Asp140Tyr | missense_variant | 4/7 | ENST00000232003.5 | |
HRG-AS1 | XR_924801.3 | n.291-19778C>A | intron_variant, non_coding_transcript_variant | ||||
HRG | XM_005247415.5 | c.418G>T | p.Asp140Tyr | missense_variant | 4/7 | ||
HRG-AS1 | XR_001741059.2 | n.291-19778C>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HRG | ENST00000232003.5 | c.418G>T | p.Asp140Tyr | missense_variant | 4/7 | 1 | NM_000412.5 | P1 | |
HRG-AS1 | ENST00000630178.2 | n.238+46818C>A | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152146Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251284Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135794
GnomAD4 exome AF: 0.0000130 AC: 19AN: 1461796Hom.: 0 Cov.: 31 AF XY: 0.0000138 AC XY: 10AN XY: 727206
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152146Hom.: 0 Cov.: 31 AF XY: 0.0000269 AC XY: 2AN XY: 74310
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 01, 2021 | The c.418G>T (p.D140Y) alteration is located in exon 4 (coding exon 4) of the HRG gene. This alteration results from a G to T substitution at nucleotide position 418, causing the aspartic acid (D) at amino acid position 140 to be replaced by a tyrosine (Y). 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