chr1-25388999-T-C
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_020485.8(RHCE):āc.916A>Gā(p.Ile306Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000437 in 1,614,034 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Consequence
NM_020485.8 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RHCE | NM_020485.8 | c.916A>G | p.Ile306Val | missense_variant | 6/10 | ENST00000294413.13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RHCE | ENST00000294413.13 | c.916A>G | p.Ile306Val | missense_variant | 6/10 | 1 | NM_020485.8 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00173 AC: 263AN: 152118Hom.: 1 Cov.: 30
GnomAD3 exomes AF: 0.000466 AC: 117AN: 251280Hom.: 0 AF XY: 0.000420 AC XY: 57AN XY: 135836
GnomAD4 exome AF: 0.000293 AC: 429AN: 1461800Hom.: 1 Cov.: 32 AF XY: 0.000237 AC XY: 172AN XY: 727202
GnomAD4 genome AF: 0.00182 AC: 277AN: 152234Hom.: 2 Cov.: 30 AF XY: 0.00191 AC XY: 142AN XY: 74446
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Oct 24, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at