1-207888710-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001025109.2(CD34):c.944G>A(p.Arg315His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000162 in 1,614,086 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000099 ( 0 hom., cov: 33)
Exomes 𝑓: 0.00017 ( 1 hom. )
Consequence
CD34
NM_001025109.2 missense
NM_001025109.2 missense
Scores
1
8
10
Clinical Significance
Conservation
PhyloP100: 1.96
Genes affected
CD34 (HGNC:1662): (CD34 molecule) The protein encoded by this gene may play a role in the attachment of stem cells to the bone marrow extracellular matrix or to stromal cells. This single-pass membrane protein is highly glycosylated and phosphorylated by protein kinase C. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Aug 2011]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (MetaRNN=0.18660119).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CD34 | NM_001025109.2 | c.944G>A | p.Arg315His | missense_variant | 7/8 | ENST00000310833.12 | |
CD34 | NM_001773.3 | c.944G>A | p.Arg315His | missense_variant | 7/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CD34 | ENST00000310833.12 | c.944G>A | p.Arg315His | missense_variant | 7/8 | 1 | NM_001025109.2 | P1 | |
CD34 | ENST00000356522.4 | c.944G>A | p.Arg315His | missense_variant | 7/8 | 1 | |||
CD34 | ENST00000367036.7 | c.470G>A | p.Arg157His | missense_variant | 4/5 | 1 | |||
CD34 | ENST00000485761.1 | n.590G>A | non_coding_transcript_exon_variant | 5/6 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000985 AC: 15AN: 152222Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.000195 AC: 49AN: 251380Hom.: 0 AF XY: 0.000221 AC XY: 30AN XY: 135848
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GnomAD4 exome AF: 0.000169 AC: 247AN: 1461864Hom.: 1 Cov.: 32 AF XY: 0.000175 AC XY: 127AN XY: 727234
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GnomAD4 genome ? AF: 0.0000985 AC: 15AN: 152222Hom.: 0 Cov.: 33 AF XY: 0.0000941 AC XY: 7AN XY: 74362
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 12, 2021 | The c.944G>A (p.R315H) alteration is located in exon 7 (coding exon 7) of the CD34 gene. This alteration results from a G to A substitution at nucleotide position 944, causing the arginine (R) at amino acid position 315 to be replaced by a histidine (H). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Pathogenic
Dann
Pathogenic
DEOGEN2
Benign
T;.;.
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Benign
D
LIST_S2
Benign
T;T;T
M_CAP
Benign
T
MetaRNN
Benign
T;T;T
MetaSVM
Benign
T
MutationAssessor
Uncertain
M;.;M
MutationTaster
Benign
D;D;D;D
PrimateAI
Uncertain
T
PROVEAN
Uncertain
D;D;D
REVEL
Uncertain
Sift
Uncertain
D;D;D
Sift4G
Uncertain
D;D;D
Polyphen
D;D;D
Vest4
MVP
MPC
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
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Score
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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