10-32922694-T-G
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 1P and 6B. PP2BP4_ModerateBS2
The NM_002211.4(ITGB1):c.984A>C(p.Glu328Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000137 in 1,606,596 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_002211.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ITGB1 | NM_002211.4 | c.984A>C | p.Glu328Asp | missense_variant | 8/16 | ENST00000302278.8 | |
ITGB1 | NM_033668.2 | c.984A>C | p.Glu328Asp | missense_variant | 7/16 | ||
ITGB1 | NM_133376.3 | c.984A>C | p.Glu328Asp | missense_variant | 8/16 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ITGB1 | ENST00000302278.8 | c.984A>C | p.Glu328Asp | missense_variant | 8/16 | 1 | NM_002211.4 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000788 AC: 12AN: 152192Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000201 AC: 5AN: 248344Hom.: 0 AF XY: 0.0000149 AC XY: 2AN XY: 134172
GnomAD4 exome AF: 0.00000688 AC: 10AN: 1454404Hom.: 0 Cov.: 28 AF XY: 0.00000415 AC XY: 3AN XY: 723754
GnomAD4 genome ? AF: 0.0000788 AC: 12AN: 152192Hom.: 0 Cov.: 32 AF XY: 0.0000942 AC XY: 7AN XY: 74336
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 03, 2022 | The c.984A>C (p.E328D) alteration is located in exon 7 (coding exon 7) of the ITGB1 gene. This alteration results from a A to C substitution at nucleotide position 984, causing the glutamic acid (E) at amino acid position 328 to be replaced by an aspartic acid (D). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at