1-38915656-A-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_017821.5(RHBDL2):c.301T>A(p.Leu101Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000514 in 1,614,120 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign 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_017821.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RHBDL2 | NM_017821.5 | c.301T>A | p.Leu101Met | missense_variant | 3/8 | ENST00000372990.6 | |
LOC105378662 | XR_001737994.2 | n.89+2028A>T | intron_variant, non_coding_transcript_variant | ||||
RHBDL2 | NM_001304746.2 | c.541T>A | p.Leu181Met | missense_variant | 3/8 | ||
LOC105378662 | XR_947215.2 | n.115+389A>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RHBDL2 | ENST00000372990.6 | c.301T>A | p.Leu101Met | missense_variant | 3/8 | 5 | NM_017821.5 | P1 | |
RRAGC-DT | ENST00000667635.1 | n.268-48478A>T | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.000263 AC: 40AN: 152142Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000437 AC: 11AN: 251458Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135904
GnomAD4 exome AF: 0.0000294 AC: 43AN: 1461860Hom.: 1 Cov.: 31 AF XY: 0.0000220 AC XY: 16AN XY: 727238
GnomAD4 genome AF: 0.000263 AC: 40AN: 152260Hom.: 0 Cov.: 31 AF XY: 0.000175 AC XY: 13AN XY: 74452
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 10, 2022 | The c.301T>A (p.L101M) alteration is located in exon 3 (coding exon 2) of the RHBDL2 gene. This alteration results from a T to A substitution at nucleotide position 301, causing the leucine (L) at amino acid position 101 to be replaced by a methionine (M). 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