4-150583675-T-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 3P and 7B. PM2PP2BP4BP6_ModerateBS1
The NM_006439.5(MAB21L2):c.646T>A(p.Tyr216Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000558 in 1,613,880 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_006439.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MAB21L2 | NM_006439.5 | c.646T>A | p.Tyr216Asn | missense_variant | 1/1 | ENST00000317605.6 | |
LRBA | NM_001364905.1 | c.6330+4373A>T | intron_variant | ENST00000651943.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MAB21L2 | ENST00000317605.6 | c.646T>A | p.Tyr216Asn | missense_variant | 1/1 | NM_006439.5 | P1 | ||
LRBA | ENST00000651943.2 | c.6330+4373A>T | intron_variant | NM_001364905.1 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152120Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000521 AC: 13AN: 249754Hom.: 0 AF XY: 0.0000665 AC XY: 9AN XY: 135384
GnomAD4 exome AF: 0.0000588 AC: 86AN: 1461642Hom.: 0 Cov.: 31 AF XY: 0.0000674 AC XY: 49AN XY: 727114
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152238Hom.: 0 Cov.: 32 AF XY: 0.0000537 AC XY: 4AN XY: 74442
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Aug 24, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at