Genetic Variant NM_001025109.2:c.*724C>T (chr1-207887014-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001025109.2(CD34):c.*724C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0859 in 152,518 control chromosomes in the GnomAD database, including 817 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.086 ( 815 hom., cov: 32)

Exomes 𝑓: 0.10 ( 2 hom. )

Consequence

CD34
NM_001025109.2 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.171

Publications

14 publications found

Variant links:

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]

CD34 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.72).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.346 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CD34	NM_001025109.2 link	c.*724C>T		3_prime_UTR_variant	Exon 8 of 8	ENST00000310833.12	NP_001020280.1	P28906-1
CD34	NM_001773.3 link	c.*1090C>T		3_prime_UTR_variant	Exon 8 of 8		NP_001764.1	P28906-2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
CD34	ENST00000310833.12 link	c.*724C>T	3_prime_UTR_variant	Exon 8 of 8	1	NM_001025109.2	ENSP00000310036.7	P28906-1
CD34	ENST00000356522.4 link	c.*1090C>T	3_prime_UTR_variant	Exon 8 of 8	1		ENSP00000348916.4	P28906-2
CD34	ENST00000367036.7 link	c.*724C>T	3_prime_UTR_variant	Exon 5 of 5	1		ENSP00000356003.3	Q5JTA5
CD34	ENST00000485761.1 link	n.618+1668C>T	intron_variant	Intron 5 of 5	5

Frequencies

GnomAD3 genomes

AF:

0.0859

AC:

13068

AN:

152090

Hom.:

818

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0581

Gnomad AMI

AF:

0.0318

Gnomad AMR

AF:

0.0603

Gnomad ASJ

AF:

0.0911

Gnomad EAS

AF:

0.359

Gnomad SAS

AF:

0.130

Gnomad FIN

AF:

0.148

Gnomad MID

AF:

0.0538

Gnomad NFE

AF:

0.0758

Gnomad OTH

AF:

0.0785

GnomAD4 exome

AF:

0.103

AC:

AN:

310

Hom.:

Cov.:

AF XY:

0.101

AC XY:

AN XY:

208

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AF:

0.00

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

East Asian (EAS)

AF:

0.500

AC:

AN:

South Asian (SAS)

AF:

0.500

AC:

AN:

European-Finnish (FIN)

AF:

0.120

AC:

AN:

142

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0786

AC:

AN:

140

Other (OTH)

AF:

0.0714

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.493

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.0859

AC:

13069

AN:

152208

Hom.:

815

Cov.:

AF XY:

0.0906

AC XY:

6741

AN XY:

74408

show subpopulations

African (AFR)

AF:

0.0581

AC:

2414

AN:

41538

American (AMR)

AF:

0.0603

AC:

922

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.0911

AC:

316

AN:

3470

East Asian (EAS)

AF:

0.359

AC:

1856

AN:

5164

South Asian (SAS)

AF:

0.130

AC:

628

AN:

4818

European-Finnish (FIN)

AF:

0.148

AC:

1570

AN:

10612

Middle Eastern (MID)

AF:

0.0510

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0758

AC:

5153

AN:

67992

Other (OTH)

AF:

0.0787

AC:

166

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

584

1167

1751

2334

2918

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

156

312

468

624

780

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0757

Hom.:

838

Bravo

AF:

0.0811

Asia WGS

AF:

0.247

AC:

855

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.72

CADD

Benign

(source)

DANN

Benign

0.82

PhyloP100

0.17

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over