chr11-72225386-A-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_001567.4(INPPL1):c.182+220A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0203 in 985,378 control chromosomes in the GnomAD database, including 237 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.020 ( 68 hom., cov: 32)
Exomes 𝑓: 0.020 ( 169 hom. )
Consequence
INPPL1
NM_001567.4 intron
NM_001567.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.905
Genes affected
INPPL1 (HGNC:6080): (inositol polyphosphate phosphatase like 1) The protein encoded by this gene is an SH2-containing 5'-inositol phosphatase that is involved in the regulation of insulin function. The encoded protein also plays a role in the regulation of epidermal growth factor receptor turnover and actin remodelling. Additionally, this gene supports metastatic growth in breast cancer and is a valuable biomarker for breast cancer. [provided by RefSeq, Jan 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.81).
BP6
?
Variant 11-72225386-A-G is Benign according to our data. Variant chr11-72225386-A-G is described in ClinVar as [Benign]. Clinvar id is 1237230.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0199 (3029/152270) while in subpopulation NFE AF= 0.0241 (1637/68020). AF 95% confidence interval is 0.0231. There are 68 homozygotes in gnomad4. There are 1662 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 67 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
INPPL1 | NM_001567.4 | c.182+220A>G | intron_variant | ENST00000298229.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
INPPL1 | ENST00000298229.7 | c.182+220A>G | intron_variant | 1 | NM_001567.4 | P1 | |||
INPPL1 | ENST00000541544.1 | n.98+220A>G | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0199 AC: 3027AN: 152152Hom.: 67 Cov.: 32
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GnomAD4 exome AF: 0.0203 AC: 16934AN: 833108Hom.: 169 Cov.: 30 AF XY: 0.0200 AC XY: 7706AN XY: 384714
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Aug 30, 2018 | - - |
Computational scores
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Cadd
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Dann
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at