chr11-67663750-C-A

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_001393402.2(ALDH3B2):​c.885G>T​(p.Gln295His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000217 in 1,611,812 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.00012 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000012 ( 0 hom. )

Consequence

ALDH3B2
NM_001393402.2 missense

Scores

19

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 0.590
Variant links:
Genes affected
ALDH3B2 (HGNC:411): (aldehyde dehydrogenase 3 family member B2) This gene encodes a member of the aldehyde dehydrogenase family, a group of isozymes that may play a major role in the detoxification of aldehydes generated by alcohol metabolism and lipid peroxidation. The gene of this particular family member is over 10 kb in length. Altered methylation patterns at this locus have been observed in spermatozoa derived from patients exhibiting reduced fecundity. [provided by RefSeq, Aug 2017]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.09639558).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ALDH3B2NM_001393402.2 linkc.885G>T p.Gln295His missense_variant Exon 9 of 10 ENST00000673966.2 NP_001380331.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ALDH3B2ENST00000673966.2 linkc.885G>T p.Gln295His missense_variant Exon 9 of 10 NM_001393402.2 ENSP00000501254.1 P48448
ALDH3B2ENST00000530069.6 linkc.885G>T p.Gln295His missense_variant Exon 9 of 10 1 ENSP00000431595.1 P48448
ALDH3B2ENST00000349015.7 linkc.885G>T p.Gln295His missense_variant Exon 9 of 10 5 ENSP00000255084.3 P48448
ALDH3B2ENST00000531248.1 linkc.159-351G>T intron_variant Intron 2 of 2 5 ENSP00000435476.1 H0YEC0

Frequencies

GnomAD3 genomes
AF:
0.000112
AC:
17
AN:
152204
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.000410
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.0000279
AC:
7
AN:
250456
Hom.:
0
AF XY:
0.0000148
AC XY:
2
AN XY:
135342
show subpopulations
Gnomad AFR exome
AF:
0.000433
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.0000116
AC:
17
AN:
1459490
Hom.:
0
Cov.:
32
AF XY:
0.0000110
AC XY:
8
AN XY:
725616
show subpopulations
Gnomad4 AFR exome
AF:
0.000478
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.0000166
GnomAD4 genome
AF:
0.000118
AC:
18
AN:
152322
Hom.:
0
Cov.:
32
AF XY:
0.000161
AC XY:
12
AN XY:
74484
show subpopulations
Gnomad4 AFR
AF:
0.000433
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.0000987
Hom.:
0
Bravo
AF:
0.000110
ESP6500AA
AF:
0.000455
AC:
2
ESP6500EA
AF:
0.00
AC:
0
ExAC
AF:
0.0000494
AC:
6
Asia WGS
AF:
0.000289
AC:
1
AN:
3478

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
Mar 18, 2024
Ambry Genetics
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The c.885G>T (p.Q295H) alteration is located in exon 9 (coding exon 7) of the ALDH3B2 gene. This alteration results from a G to T substitution at nucleotide position 885, causing the glutamine (Q) at amino acid position 295 to be replaced by a histidine (H). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.17
BayesDel_addAF
Benign
-0.37
T
BayesDel_noAF
Benign
-0.46
CADD
Benign
14
DANN
Benign
0.94
DEOGEN2
Benign
0.077
T;T
Eigen
Benign
-0.65
Eigen_PC
Benign
-0.65
FATHMM_MKL
Benign
0.31
N
LIST_S2
Benign
0.72
.;T
M_CAP
Benign
0.015
T
MetaRNN
Benign
0.096
T;T
MetaSVM
Benign
-0.41
T
MutationAssessor
Benign
0.41
N;N
PrimateAI
Benign
0.26
T
PROVEAN
Benign
-1.8
N;N
REVEL
Benign
0.19
Sift
Benign
0.11
T;T
Sift4G
Benign
0.11
T;T
Polyphen
0.0060
B;B
Vest4
0.32
MutPred
0.51
Gain of catalytic residue at Q295 (P = 0.0188);Gain of catalytic residue at Q295 (P = 0.0188);
MVP
0.77
MPC
0.21
ClinPred
0.054
T
GERP RS
3.6
Varity_R
0.24
gMVP
0.58

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: rs141299989; hg19: chr11-67431221; API