chr1-38919202-A-G
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_017821.5(RHBDL2):āc.11T>Cā(p.Val4Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000781 in 1,613,962 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Consequence
NM_017821.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RHBDL2 | NM_017821.5 | c.11T>C | p.Val4Ala | missense_variant | 2/8 | ENST00000372990.6 | |
LOC105378662 | XR_001737994.2 | n.118A>G | non_coding_transcript_exon_variant | 2/2 | |||
RHBDL2 | NM_001304746.2 | c.251T>C | p.Val84Ala | missense_variant | 2/8 | ||
LOC105378662 | XR_947215.2 | n.144A>G | non_coding_transcript_exon_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RHBDL2 | ENST00000372990.6 | c.11T>C | p.Val4Ala | missense_variant | 2/8 | 5 | NM_017821.5 | P1 | |
RRAGC-DT | ENST00000667635.1 | n.268-44932A>G | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152070Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000398 AC: 10AN: 251468Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135904
GnomAD4 exome AF: 0.0000814 AC: 119AN: 1461892Hom.: 0 Cov.: 31 AF XY: 0.0000866 AC XY: 63AN XY: 727246
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152070Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74268
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at