chr17-9917932-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_201433.2(GAS7):c.1317+69G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.47 in 1,105,584 control chromosomes in the GnomAD database, including 127,960 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.39 ( 13439 hom., cov: 34)
Exomes 𝑓: 0.48 ( 114521 hom. )
Consequence
GAS7
NM_201433.2 intron
NM_201433.2 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.77
Genes affected
GAS7 (HGNC:4169): (growth arrest specific 7) Growth arrest-specific 7 is expressed primarily in terminally differentiated brain cells and predominantly in mature cerebellar Purkinje neurons. GAS7 plays a putative role in neuronal development. Several transcript variants encoding proteins which vary in the N-terminus have been described. [provided by RefSeq, Jul 2008]
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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=-0.97).
BP6
?
Variant 17-9917932-C-T is Benign according to our data. Variant chr17-9917932-C-T is described in ClinVar as [Benign]. Clinvar id is 1271504.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.51 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GAS7 | NM_201433.2 | c.1317+69G>A | intron_variant | ENST00000432992.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GAS7 | ENST00000432992.7 | c.1317+69G>A | intron_variant | 1 | NM_201433.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.387 AC: 58892AN: 152050Hom.: 13442 Cov.: 34
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GnomAD4 exome AF: 0.484 AC: 461207AN: 953414Hom.: 114521 AF XY: 0.482 AC XY: 235242AN XY: 488124
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GnomAD4 genome ? AF: 0.387 AC: 58889AN: 152170Hom.: 13439 Cov.: 34 AF XY: 0.384 AC XY: 28550AN XY: 74380
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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 | Jun 18, 2021 | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at