chr1-25402721-T-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_020485.8(RHCE):c.361A>T(p.Met121Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00107 in 1,613,988 control chromosomes in the GnomAD database, including 20 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 (★).
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.361A>T | p.Met121Leu | missense_variant | 3/10 | ENST00000294413.13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RHCE | ENST00000294413.13 | c.361A>T | p.Met121Leu | missense_variant | 3/10 | 1 | NM_020485.8 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00112 AC: 171AN: 152004Hom.: 0 Cov.: 30
GnomAD3 exomes AF: 0.00179 AC: 449AN: 251466Hom.: 3 AF XY: 0.00195 AC XY: 265AN XY: 135910
GnomAD4 exome AF: 0.00106 AC: 1551AN: 1461866Hom.: 20 Cov.: 32 AF XY: 0.00114 AC XY: 827AN XY: 727236
GnomAD4 genome AF: 0.00112 AC: 171AN: 152122Hom.: 0 Cov.: 30 AF XY: 0.00144 AC XY: 107AN XY: 74372
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Sep 01, 2023 | RHCE: BP4 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at