rs2284235

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_006020.3(ALKBH1):​c.293-2180A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.366 in 186,724 control chromosomes in the GnomAD database, including 12,699 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 0.35 ( 9417 hom., cov: 32)
Exomes 𝑓: 0.45 ( 3282 hom. )

Consequence

ALKBH1
NM_006020.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.74
Variant links:
Genes affected
ALKBH1 (HGNC:17911): (alkB homolog 1, histone H2A dioxygenase) This gene encodes a homolog to the E. coli alkB gene product. The E. coli alkB protein is part of the adaptive response mechanism of DNA alkylation damage repair. It is involved in damage reversal by oxidative demethylation of 1-methyladenine and 3-methylcytosine. [provided by RefSeq, Jul 2008]
ZMYND19P1 (HGNC:44540): (zinc finger MYND-type containing 19 pseudogene 1)

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.75).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.393 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ALKBH1NM_006020.3 linkuse as main transcriptc.293-2180A>G intron_variant ENST00000216489.8
ALKBH1XM_047431848.1 linkuse as main transcriptc.293-2180A>G intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ALKBH1ENST00000216489.8 linkuse as main transcriptc.293-2180A>G intron_variant 1 NM_006020.3 P1
ZMYND19P1ENST00000554267.1 linkuse as main transcriptn.490T>C non_coding_transcript_exon_variant 1/1

Frequencies

GnomAD3 genomes
AF:
0.347
AC:
52623
AN:
151850
Hom.:
9413
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.282
Gnomad AMI
AF:
0.284
Gnomad AMR
AF:
0.306
Gnomad ASJ
AF:
0.451
Gnomad EAS
AF:
0.317
Gnomad SAS
AF:
0.284
Gnomad FIN
AF:
0.346
Gnomad MID
AF:
0.358
Gnomad NFE
AF:
0.397
Gnomad OTH
AF:
0.347
GnomAD4 exome
AF:
0.454
AC:
15780
AN:
34756
Hom.:
3282
Cov.:
0
AF XY:
0.457
AC XY:
9434
AN XY:
20630
show subpopulations
Gnomad4 AFR exome
AF:
0.373
Gnomad4 AMR exome
AF:
0.360
Gnomad4 ASJ exome
AF:
0.507
Gnomad4 EAS exome
AF:
0.382
Gnomad4 SAS exome
AF:
0.390
Gnomad4 FIN exome
AF:
0.473
Gnomad4 NFE exome
AF:
0.499
Gnomad4 OTH exome
AF:
0.470
GnomAD4 genome
AF:
0.346
AC:
52646
AN:
151968
Hom.:
9417
Cov.:
32
AF XY:
0.344
AC XY:
25515
AN XY:
74250
show subpopulations
Gnomad4 AFR
AF:
0.282
Gnomad4 AMR
AF:
0.305
Gnomad4 ASJ
AF:
0.451
Gnomad4 EAS
AF:
0.316
Gnomad4 SAS
AF:
0.284
Gnomad4 FIN
AF:
0.346
Gnomad4 NFE
AF:
0.397
Gnomad4 OTH
AF:
0.350
Alfa
AF:
0.367
Hom.:
2159
Bravo
AF:
0.337
Asia WGS
AF:
0.308
AC:
1073
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.75
CADD
Benign
5.3
DANN
Benign
0.72

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs2284235; hg19: chr14-78163423; COSMIC: COSV53659445; API