chr19-4363173-G-T
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_003025.4(SH3GL1):c.728+197C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.623 in 152,048 control chromosomes in the GnomAD database, including 29,923 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.62 ( 29923 hom., cov: 33)
Consequence
SH3GL1
NM_003025.4 intron
NM_003025.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.59
Genes affected
SH3GL1 (HGNC:10830): (SH3 domain containing GRB2 like 1, endophilin A2) This gene encodes a member of the endophilin family of Src homology 3 domain-containing proteins. The encoded protein is involved in endocytosis and may also play a role in the cell cycle. Overexpression of this gene may play a role in leukemogenesis, and the encoded protein has been implicated in acute myeloid leukemia as a fusion partner of the myeloid-lymphoid leukemia protein. Pseudogenes of this gene are located on the long arm of chromosomes 11 and 17. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Jan 2011]
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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=-1.05).
BP6
Variant 19-4363173-G-T is Benign according to our data. Variant chr19-4363173-G-T is described in ClinVar as [Benign]. Clinvar id is 1222997.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.719 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SH3GL1 | NM_003025.4 | c.728+197C>A | intron_variant | ENST00000269886.7 | NP_003016.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SH3GL1 | ENST00000269886.7 | c.728+197C>A | intron_variant | 1 | NM_003025.4 | ENSP00000269886.2 | ||||
SH3GL1 | ENST00000417295.6 | c.584+197C>A | intron_variant | 2 | ENSP00000404568.2 | |||||
SH3GL1 | ENST00000598564.5 | c.536+197C>A | intron_variant | 2 | ENSP00000470792.1 |
Frequencies
GnomAD3 genomes AF: 0.623 AC: 94593AN: 151930Hom.: 29876 Cov.: 33
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.623 AC: 94695AN: 152048Hom.: 29923 Cov.: 33 AF XY: 0.623 AC XY: 46334AN XY: 74340
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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 | Nov 12, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at