chr20-37384650-A-G
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_198291.3(SRC):c.250+247A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 1.0 ( 75884 hom., cov: 30)
Failed GnomAD Quality Control
Consequence
SRC
NM_198291.3 intron
NM_198291.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.616
Genes affected
SRC (HGNC:11283): (SRC proto-oncogene, non-receptor tyrosine kinase) This gene is highly similar to the v-src gene of Rous sarcoma virus. This proto-oncogene may play a role in the regulation of embryonic development and cell growth. The protein encoded by this gene is a tyrosine-protein kinase whose activity can be inhibited by phosphorylation by c-SRC kinase. Mutations in this gene could be involved in the malignant progression of colon cancer. Two transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BP6
?
Variant 20-37384650-A-G is Benign according to our data. Variant chr20-37384650-A-G is described in ClinVar as [Benign]. Clinvar id is 1276301.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
?
High AC in GnomAd at 151686 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SRC | NM_198291.3 | c.250+247A>G | intron_variant | ENST00000373578.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SRC | ENST00000373578.7 | c.250+247A>G | intron_variant | 5 | NM_198291.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 1.00 AC: 151686AN: 151712Hom.: 75830 Cov.: 30
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? Data not reliable, filtered out with message: AS_VQSR AF: 1.00 AC: 151794AN: 151820Hom.: 75884 Cov.: 30 AF XY: 1.00 AC XY: 74182AN XY: 74196
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?
Data not reliable, filtered out with message: AS_VQSR
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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 19, 2021 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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