rs2556

chr1-207887014-G-Achr1-207887014-G-C

Variant summary

Our verdict is Benign. Variant got -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

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 Benign. Variant got -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/exons	MANE	UniProt
CD34	NM_001025109.2	c.*724C>T		3_prime_UTR_variant	8/8	ENST00000310833.12
CD34	NM_001773.3	c.*1090C>T		3_prime_UTR_variant	8/8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CD34	ENST00000310833.12	c.*724C>T		3_prime_UTR_variant	8/8	1	NM_001025109.2	P1
CD34	ENST00000356522.4	c.*1090C>T		3_prime_UTR_variant	8/8	1
CD34	ENST00000367036.7	c.*724C>T		3_prime_UTR_variant	5/5	1
CD34	ENST00000485761.1	n.618+1668C>T		intron_variant, non_coding_transcript_variant		5

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

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.500

Gnomad4 SAS exome AF: 0.500

Gnomad4 FIN exome AF: 0.120

Gnomad4 NFE exome AF: 0.0786

Gnomad4 OTH exome AF: 0.0714

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

Gnomad4 AFR AF: 0.0581

Gnomad4 AMR AF: 0.0603

Gnomad4 ASJ AF: 0.0911

Gnomad4 EAS AF: 0.359

Gnomad4 SAS AF: 0.130

Gnomad4 FIN AF: 0.148

Gnomad4 NFE AF: 0.0758

Gnomad4 OTH AF: 0.0787

Alfa AF: 0.0767 Hom.: 676

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	10
Dann	Benign	0.82

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

LitVar

Other links and lift over

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