chr3-186671650-A-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_000412.5(HRG):c.419A>T(p.Asp140Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000471 in 1,614,112 control chromosomes in the GnomAD database, with no homozygous occurrence. 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. D140Y) has been classified as Uncertain significance.
Frequency
Consequence
NM_000412.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HRG | NM_000412.5 | c.419A>T | p.Asp140Val | missense_variant | 4/7 | ENST00000232003.5 | |
HRG-AS1 | XR_924801.3 | n.291-19779T>A | intron_variant, non_coding_transcript_variant | ||||
HRG | XM_005247415.5 | c.419A>T | p.Asp140Val | missense_variant | 4/7 | ||
HRG-AS1 | XR_001741059.2 | n.291-19779T>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HRG | ENST00000232003.5 | c.419A>T | p.Asp140Val | missense_variant | 4/7 | 1 | NM_000412.5 | P1 | |
HRG-AS1 | ENST00000630178.2 | n.238+46817T>A | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.000283 AC: 43AN: 152186Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000875 AC: 22AN: 251290Hom.: 0 AF XY: 0.0000663 AC XY: 9AN XY: 135800
GnomAD4 exome AF: 0.0000226 AC: 33AN: 1461808Hom.: 0 Cov.: 31 AF XY: 0.0000179 AC XY: 13AN XY: 727212
GnomAD4 genome ? AF: 0.000282 AC: 43AN: 152304Hom.: 0 Cov.: 31 AF XY: 0.000282 AC XY: 21AN XY: 74474
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 14, 2021 | The c.419A>T (p.D140V) alteration is located in exon 4 (coding exon 4) of the HRG gene. This alteration results from a A to T substitution at nucleotide position 419, causing the aspartic acid (D) at amino acid position 140 to be replaced by a valine (V). 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