chr14-77675758-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_006020.3(ALKBH1):c.638G>A(p.Arg213Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000242 in 1,613,952 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_006020.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ALKBH1 | NM_006020.3 | c.638G>A | p.Arg213Gln | missense_variant | 5/6 | ENST00000216489.8 | NP_006011.2 | |
ALKBH1 | XM_047431848.1 | c.*28G>A | 3_prime_UTR_variant | 5/5 | XP_047287804.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ALKBH1 | ENST00000216489.8 | c.638G>A | p.Arg213Gln | missense_variant | 5/6 | 1 | NM_006020.3 | ENSP00000216489 | P1 | |
ALKBH1 | ENST00000555100.1 | c.*69G>A | 3_prime_UTR_variant, NMD_transcript_variant | 4/5 | 3 | ENSP00000451386 | ||||
ALKBH1 | ENST00000557057.5 | c.*124G>A | 3_prime_UTR_variant, NMD_transcript_variant | 4/5 | 3 | ENSP00000451886 |
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152084Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000318 AC: 8AN: 251482Hom.: 0 AF XY: 0.0000294 AC XY: 4AN XY: 135912
GnomAD4 exome AF: 0.0000212 AC: 31AN: 1461868Hom.: 0 Cov.: 31 AF XY: 0.0000206 AC XY: 15AN XY: 727236
GnomAD4 genome AF: 0.0000526 AC: 8AN: 152084Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74290
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | May 02, 2024 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at