chr11-18465700-G-A
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Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_144972.5(LDHAL6A):c.308G>A(p.Gly103Glu) variant causes a missense change. The variant allele was found at a frequency of 0.0000273 in 1,613,998 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.00018 ( 0 hom., cov: 31)
Exomes 𝑓: 0.000012 ( 0 hom. )
Consequence
LDHAL6A
NM_144972.5 missense
NM_144972.5 missense
Scores
10
6
3
Clinical Significance
Conservation
PhyloP100: 6.78
Genes affected
LDHAL6A (HGNC:28335): (lactate dehydrogenase A like 6A) Predicted to enable L-lactate dehydrogenase activity. Predicted to be involved in carbohydrate metabolic process and carboxylic acid metabolic process. Located in extracellular exosome. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 4 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PP3
MetaRNN computational evidence supports a deleterious effect, 0.874
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LDHAL6A | NM_144972.5 | c.308G>A | p.Gly103Glu | missense_variant | 3/7 | ENST00000280706.3 | NP_659409.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LDHAL6A | ENST00000280706.3 | c.308G>A | p.Gly103Glu | missense_variant | 3/7 | 2 | NM_144972.5 | ENSP00000280706 | P1 | |
LDHAL6A | ENST00000396213.7 | c.308G>A | p.Gly103Glu | missense_variant | 4/8 | 1 | ENSP00000379516 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000171 AC: 26AN: 152134Hom.: 0 Cov.: 31
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GnomAD3 exomes AF: 0.0000199 AC: 5AN: 251444Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135902
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GnomAD4 exome AF: 0.0000116 AC: 17AN: 1461746Hom.: 0 Cov.: 30 AF XY: 0.00000688 AC XY: 5AN XY: 727190
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GnomAD4 genome AF: 0.000177 AC: 27AN: 152252Hom.: 0 Cov.: 31 AF XY: 0.000188 AC XY: 14AN XY: 74456
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 18, 2021 | The c.308G>A (p.G103E) alteration is located in exon 3 (coding exon 3) of the LDHAL6A gene. This alteration results from a G to A substitution at nucleotide position 308, causing the glycine (G) at amino acid position 103 to be replaced by a glutamic acid (E). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Uncertain
T
BayesDel_noAF
Pathogenic
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Pathogenic
.;D;D
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Pathogenic
D;.;D
M_CAP
Uncertain
D
MetaRNN
Pathogenic
D;D;D
MetaSVM
Pathogenic
D
MutationAssessor
Pathogenic
.;M;M
MutationTaster
Benign
D;D
PrimateAI
Benign
T
PROVEAN
Pathogenic
.;D;D
REVEL
Pathogenic
Sift
Pathogenic
.;D;D
Sift4G
Uncertain
D;D;D
Polyphen
0.99
.;D;D
Vest4
MutPred
Gain of solvent accessibility (P = 0.024);Gain of solvent accessibility (P = 0.024);Gain of solvent accessibility (P = 0.024);
MVP
MPC
0.50
ClinPred
D
GERP RS
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gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
DS_DG_spliceai
Position offset: 31
Find out detailed SpliceAI scores and Pangolin per-transcript scores at