rs2556

Variant names:

• chr1-207887014-G-A
• rs2556
• NM_001025109.2:c.*724C>T

Your query was ambiguous. Multiple possible variants found:

• chr1-207887014-G-A
• chr1-207887014-G-C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.171
• Publications: 14 publications found

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

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001025109.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD34	NM_001025109.2	MANE Select	c.*724C>T		3_prime_UTR	Exon 8 of 8	NP_001020280.1
	CD34	NM_001773.3		c.*1090C>T		3_prime_UTR	Exon 8 of 8	NP_001764.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD34	ENST00000310833.12	TSL:1 MANE Select	c.*724C>T		3_prime_UTR	Exon 8 of 8	ENSP00000310036.7
	CD34	ENST00000356522.4	TSL:1	c.*1090C>T		3_prime_UTR	Exon 8 of 8	ENSP00000348916.4
	CD34	ENST00000367036.7	TSL:1	c.*724C>T		3_prime_UTR	Exon 5 of 5	ENSP00000356003.3

Frequencies

GnomAD3 genomes AF: 0.0859 AC: 13068 AN: 152090 Hom.: 818 Cov.: 32

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: 32 AN: 310 Hom.: 2 Cov.: 0 AF XY: 0.101 AC XY: 21 AN XY: 208

African (AFR) AF: 0.00 AC: 0 AN: 2

American (AMR) AF: 0.00 AC: 0 AN: 2

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2

East Asian (EAS) AF: 0.500 AC: 2 AN: 4

South Asian (SAS) AF: 0.500 AC: 1 AN: 2

European-Finnish (FIN) AF: 0.120 AC: 17 AN: 142

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2

European-Non Finnish (NFE) AF: 0.0786 AC: 11 AN: 140

Other (OTH) AF: 0.0714 AC: 1 AN: 14

GnomAD4 genome AF: 0.0859 AC: 13069 AN: 152208 Hom.: 815 Cov.: 32 AF XY: 0.0906 AC XY: 6741 AN XY: 74408

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: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0758 AC: 5153 AN: 67992

Other (OTH) AF: 0.0787 AC: 166 AN: 2110

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	10
DANN	Benign	0.82
PhyloP100		0.17
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2556; hg19: chr1-208060359; COSMIC: COSV60412807;