rs3213837
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001253697.2(ERBIN):c.821C>T(p.Ser274Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.151 in 1,602,994 control chromosomes in the GnomAD database, including 19,931 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt. Synonymous variant affecting the same amino acid position (i.e. S274S) has been classified as Likely benign.
Frequency
Consequence
NM_001253697.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ERBIN | NM_001253697.2 | c.821C>T | p.Ser274Leu | missense_variant | 11/26 | ENST00000284037.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ERBIN | ENST00000284037.10 | c.821C>T | p.Ser274Leu | missense_variant | 11/26 | 1 | NM_001253697.2 | A1 |
Frequencies
GnomAD3 genomes AF: 0.120 AC: 18257AN: 151674Hom.: 1414 Cov.: 32
GnomAD3 exomes AF: 0.153 AC: 38297AN: 250684Hom.: 3343 AF XY: 0.158 AC XY: 21414AN XY: 135592
GnomAD4 exome AF: 0.154 AC: 223650AN: 1451202Hom.: 18520 Cov.: 29 AF XY: 0.157 AC XY: 113606AN XY: 722652
GnomAD4 genome AF: 0.120 AC: 18249AN: 151792Hom.: 1411 Cov.: 32 AF XY: 0.121 AC XY: 9004AN XY: 74180
ClinVar
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan | Jan 24, 2024 | This variant is classified as Benign based on local population frequency. This variant was detected in 31% of patients studied by a panel of primary immunodeficiencies. Number of patients: 27. Only high quality variants are reported. - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at