rs147654123
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 1P and 16B. PP2BP4_StrongBP6_Very_StrongBS2
The NM_012156.2(EPB41L1):c.1451C>T(p.Pro484Leu) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0035 in 1,613,990 control chromosomes in the GnomAD database, including 11 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/23 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_012156.2 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -15 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EPB41L1 | NM_012156.2 | c.1451C>T | p.Pro484Leu | missense_variant, splice_region_variant | 13/22 | ENST00000338074.7 | |
LOC124904892 | XR_007067571.1 | n.264+1352G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EPB41L1 | ENST00000338074.7 | c.1451C>T | p.Pro484Leu | missense_variant, splice_region_variant | 13/22 | 1 | NM_012156.2 | P5 |
Frequencies
GnomAD3 genomes AF: 0.00199 AC: 303AN: 152036Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.00172 AC: 433AN: 251384Hom.: 1 AF XY: 0.00167 AC XY: 227AN XY: 135884
GnomAD4 exome AF: 0.00365 AC: 5337AN: 1461836Hom.: 10 Cov.: 32 AF XY: 0.00348 AC XY: 2534AN XY: 727228
GnomAD4 genome AF: 0.00200 AC: 304AN: 152154Hom.: 1 Cov.: 32 AF XY: 0.00167 AC XY: 124AN XY: 74404
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jan 01, 2023 | EPB41L1: BS1, BS2 - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Mar 03, 2017 | - - |
EPB41L1-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | May 01, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at