rs3746972
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_000211.5(ITGB2):c.148-825T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.166 in 591,072 control chromosomes in the GnomAD database, including 8,693 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_000211.5 intron
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ITGB2 | NM_000211.5 | c.148-825T>C | intron_variant | Intron 3 of 15 | ENST00000652462.1 | NP_000202.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ITGB2 | ENST00000652462.1 | c.148-825T>C | intron_variant | Intron 3 of 15 | NM_000211.5 | ENSP00000498780.1 |
Frequencies
GnomAD3 genomes AF: 0.170 AC: 25908AN: 152170Hom.: 2371 Cov.: 33
GnomAD4 exome AF: 0.164 AC: 72060AN: 438784Hom.: 6325 AF XY: 0.160 AC XY: 37301AN XY: 232866
GnomAD4 genome AF: 0.170 AC: 25913AN: 152288Hom.: 2368 Cov.: 33 AF XY: 0.171 AC XY: 12745AN XY: 74470
ClinVar
Submissions by phenotype
not specified Benign:1
This variant is classified as Benign based on local population frequency. This variant was detected in 32% of patients studied by a panel of primary immunodeficiencies. Number of patients: 30. Only high quality variants are reported. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at