chr10-32923577-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_002211.4(ITGB1):c.942+8C>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00977 in 1,603,052 control chromosomes in the GnomAD database, including 112 homozygotes. In-silico tool predicts 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 Benign (★).
Frequency
Consequence
NM_002211.4 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ITGB1 | NM_002211.4 | c.942+8C>T | splice_region_variant, intron_variant | ENST00000302278.8 | |||
ITGB1 | NM_033668.2 | c.942+8C>T | splice_region_variant, intron_variant | ||||
ITGB1 | NM_133376.3 | c.942+8C>T | splice_region_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ITGB1 | ENST00000302278.8 | c.942+8C>T | splice_region_variant, intron_variant | 1 | NM_002211.4 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.00765 AC: 1163AN: 152064Hom.: 7 Cov.: 32
GnomAD3 exomes AF: 0.00978 AC: 2414AN: 246818Hom.: 14 AF XY: 0.0108 AC XY: 1435AN XY: 133356
GnomAD4 exome AF: 0.00999 AC: 14493AN: 1450870Hom.: 105 Cov.: 29 AF XY: 0.0104 AC XY: 7528AN XY: 721556
GnomAD4 genome ? AF: 0.00764 AC: 1163AN: 152182Hom.: 7 Cov.: 32 AF XY: 0.00761 AC XY: 566AN XY: 74406
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at