chr1-207904893-G-A

Variant names:

• chr1-207904893-G-A
• rs1932819
• NM_001025109.2:c.80-4890C>T

Variant summary

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

The NM_001025109.2(CD34):​c.80-4890C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.149 in 152,164 control chromosomes in the GnomAD database, including 2,921 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 0.15 (2921 hom., cov: 33)
• Consequence: CD34 NM_001025109.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.100
• Publications: 5 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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.342 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD34	NM_001025109.2	MANE Select	c.80-4890C>T		intron	N/A	NP_001020280.1
	CD34	NM_001773.3		c.80-4890C>T		intron	N/A	NP_001764.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD34	ENST00000310833.12	TSL:1 MANE Select	c.80-4890C>T		intron	N/A	ENSP00000310036.7
	CD34	ENST00000356522.4	TSL:1	c.80-4890C>T		intron	N/A	ENSP00000348916.4

Frequencies

GnomAD3 genomes AF: 0.149 AC: 22709 AN: 152046 Hom.: 2908 Cov.: 33

Gnomad AFR AF: 0.347

Gnomad AMI AF: 0.0296

Gnomad AMR AF: 0.0960

Gnomad ASJ AF: 0.0972

Gnomad EAS AF: 0.218

Gnomad SAS AF: 0.104

Gnomad FIN AF: 0.0339

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.0615

Gnomad OTH AF: 0.147

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.149 AC: 22744 AN: 152164 Hom.: 2921 Cov.: 33 AF XY: 0.146 AC XY: 10887 AN XY: 74414

African (AFR) AF: 0.347 AC: 14388 AN: 41450

American (AMR) AF: 0.0962 AC: 1472 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0972 AC: 337 AN: 3468

East Asian (EAS) AF: 0.218 AC: 1128 AN: 5184

South Asian (SAS) AF: 0.102 AC: 492 AN: 4816

European-Finnish (FIN) AF: 0.0339 AC: 360 AN: 10612

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.0615 AC: 4180 AN: 68018

Other (OTH) AF: 0.147 AC: 311 AN: 2112

Alfa AF: 0.0953 Hom.: 3326

Bravo AF: 0.160

Asia WGS AF: 0.182 AC: 634 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.96
DANN	Benign	0.17
PhyloP100		0.10
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: rs1932819; hg19: chr1-208078238;