NM_001025109.2:c.353G>C

Variant names:

• chr1-207899136-C-G
• NM_001025109.2:c.353G>C

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001025109.2(CD34):​c.353G>C​(p.Ser118Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S118N) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 33)
• Consequence: CD34 NM_001025109.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.95

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]

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.030368537).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CD34	NM_001025109.2	c.353G>C	p.Ser118Thr	missense_variant	Exon 3 of 8	ENST00000310833.12	NP_001020280.1
CD34	NM_001773.3	c.353G>C	p.Ser118Thr	missense_variant	Exon 3 of 8		NP_001764.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CD34	ENST00000310833.12	c.353G>C	p.Ser118Thr	missense_variant	Exon 3 of 8	1	NM_001025109.2	ENSP00000310036.7
CD34	ENST00000356522.4	c.353G>C	p.Ser118Thr	missense_variant	Exon 3 of 8	1		ENSP00000348916.4
CD34	ENST00000485761.1	n.-2G>C		upstream_gene_variant		5

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.057
BayesDel_addAF	Benign	-0.43	T
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.0030
DANN	Benign	0.082
DEOGEN2	Benign	0.12	T;.
Eigen	Benign	-1.9
Eigen_PC	Benign	-2.0
FATHMM_MKL	Benign	0.0011	N
LIST_S2	Benign	0.10	T;T
M_CAP	Benign	0.0027	T
MetaRNN	Benign	0.030	T;T
MetaSVM	Benign	-0.96	T
MutationAssessor	Benign	-1.1	N;N
PrimateAI	Benign	0.26	T
PROVEAN	Benign	1.0	N;N
REVEL	Benign	0.011
Sift	Benign	0.60	T;T
Sift4G	Benign	1.0	T;T
Polyphen		0.0	B;B
Vest4		0.064
MutPred		0.28		Gain of glycosylation at T119 (P = 0.0909);Gain of glycosylation at T119 (P = 0.0909);
MVP		0.22
MPC		0.17
ClinPred		0.037	T
GERP RS		-6.8
Varity_R		0.032
gMVP		0.17

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.040		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr1-208072481;