1-156815752-AC-A
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1
The NM_003975.4(SH2D2A):c.123+253del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00392 in 1,551,468 control chromosomes in the GnomAD database, including 212 homozygotes. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.021 ( 121 hom., cov: 32)
Exomes 𝑓: 0.0021 ( 91 hom. )
Consequence
SH2D2A
NM_003975.4 intron
NM_003975.4 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -1.01
Genes affected
SH2D2A (HGNC:10821): (SH2 domain containing 2A) This gene encodes an adaptor protein thought to function in T-cell signal transduction. A related protein in mouse is responsible for the activation of lymphocyte-specific protein-tyrosine kinase and functions in downstream signaling. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2010]
NTRK1 (HGNC:8031): (neurotrophic receptor tyrosine kinase 1) This gene encodes a member of the neurotrophic tyrosine kinase receptor (NTKR) family. This kinase is a membrane-bound receptor that, upon neurotrophin binding, phosphorylates itself and members of the MAPK pathway. The presence of this kinase leads to cell differentiation and may play a role in specifying sensory neuron subtypes. Mutations in this gene have been associated with congenital insensitivity to pain, anhidrosis, self-mutilating behavior, cognitive disability and cancer. Alternate transcriptional splice variants of this gene have been found, but only three have been characterized to date. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
Variant 1-156815752-AC-A is Benign according to our data. Variant chr1-156815752-AC-A is described in ClinVar as [Benign]. Clinvar id is 1221990.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0693 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SH2D2A | NM_003975.4 | c.123+253del | intron_variant | ENST00000368199.8 | NP_003966.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SH2D2A | ENST00000368199.8 | c.123+253del | intron_variant | 1 | NM_003975.4 | ENSP00000357182 | P2 |
Frequencies
GnomAD3 genomes AF: 0.0207 AC: 3145AN: 152134Hom.: 121 Cov.: 32
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GnomAD4 exome AF: 0.00210 AC: 2936AN: 1399216Hom.: 91 Cov.: 25 AF XY: 0.00177 AC XY: 1236AN XY: 699920
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GnomAD4 genome AF: 0.0207 AC: 3149AN: 152252Hom.: 121 Cov.: 32 AF XY: 0.0201 AC XY: 1500AN XY: 74446
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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 | Mar 26, 2020 | - - |
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at