chr1-25301000-C-G
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 1P and 4B. PP3BS2
The NM_016124.6(RHD):c.541C>G(p.Leu181Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000136 in 1,246,826 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a pathogenic outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_016124.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RHD | NM_016124.6 | c.541C>G | p.Leu181Val | missense_variant | 4/10 | ENST00000328664.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RHD | ENST00000328664.9 | c.541C>G | p.Leu181Val | missense_variant | 4/10 | 1 | NM_016124.6 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 21
GnomAD3 exomes AF: 0.0000356 AC: 8AN: 224836Hom.: 3 AF XY: 0.0000330 AC XY: 4AN XY: 121116
GnomAD4 exome AF: 0.0000136 AC: 17AN: 1246826Hom.: 5 Cov.: 31 AF XY: 0.0000161 AC XY: 10AN XY: 621842
GnomAD4 genome ? Cov.: 21
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 01, 2022 | The c.541C>G (p.L181V) alteration is located in exon 4 (coding exon 4) of the RHD gene. This alteration results from a C to G substitution at nucleotide position 541, causing the leucine (L) at amino acid position 181 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