rs3890995

Variant names:

• chr12-109095724-T-C
• rs3890995
• ENST00000861370.1:c.-152+2573A>G

Variant summary

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

The ENST00000861370.1(ALKBH2):​c.-152+2573A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.189 in 152,216 control chromosomes in the GnomAD database, including 2,726 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 0.19 (2726 hom., cov: 33)
• Consequence: ALKBH2 ENST00000861370.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.596
• Publications: 12 publications found

Genes affected

ALKBH2 (HGNC:32487): (alkB homolog 2, alpha-ketoglutarate dependent dioxygenase) The Escherichia coli AlkB protein protects against the cytotoxicity of methylating agents by repair of the specific DNA lesions generated in single-stranded DNA. ALKBH2 and ALKBH3 (MIM 610603) are E. coli AlkB homologs that catalyze the removal of 1-methyladenine and 3-methylcytosine (Duncan et al., 2002 [PubMed 12486230]).[supplied by OMIM, Mar 2008]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.308 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000861370.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ALKBH2	ENST00000861370.1		c.-152+2573A>G		intron	N/A	ENSP00000531429.1
	ALKBH2	ENST00000861371.1		c.-2+2573A>G		intron	N/A	ENSP00000531430.1
	ALKBH2	ENST00000861372.1		c.-2+1883A>G		intron	N/A	ENSP00000531431.1

Frequencies

GnomAD3 genomes AF: 0.189 AC: 28747 AN: 152098 Hom.: 2724 Cov.: 33

Gnomad AFR AF: 0.171

Gnomad AMI AF: 0.138

Gnomad AMR AF: 0.177

Gnomad ASJ AF: 0.246

Gnomad EAS AF: 0.321

Gnomad SAS AF: 0.268

Gnomad FIN AF: 0.200

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.184

Gnomad OTH AF: 0.175

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

GnomAD4 genome AF: 0.189 AC: 28752 AN: 152216 Hom.: 2726 Cov.: 33 AF XY: 0.191 AC XY: 14245 AN XY: 74432

African (AFR) AF: 0.170 AC: 7077 AN: 41524

American (AMR) AF: 0.177 AC: 2709 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.246 AC: 852 AN: 3468

East Asian (EAS) AF: 0.321 AC: 1662 AN: 5176

South Asian (SAS) AF: 0.268 AC: 1295 AN: 4824

European-Finnish (FIN) AF: 0.200 AC: 2121 AN: 10592

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.184 AC: 12487 AN: 68014

Other (OTH) AF: 0.178 AC: 375 AN: 2112

Alfa AF: 0.187 Hom.: 1815

Bravo AF: 0.183

Asia WGS AF: 0.263 AC: 914 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.59
DANN	Benign	0.81
PhyloP100		-0.60

Splicing

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

Other links and lift over

dbSNP: rs3890995; hg19: chr12-109533529;