rs77290575

Variant names:

• chr16-30070155-C-G
• NM_001243177.4:c.1200C>G

Your query was ambiguous. Multiple possible variants found:

• chr16-30070155-C-G
• chr16-30070155-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_001243177.4(ALDOA):​c.1200C>G​(p.Ser400Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: ALDOA NM_001243177.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.19

Genes affected

ALDOA (HGNC:414): (aldolase, fructose-bisphosphate A) This gene encodes a member of the class I fructose-bisphosphate aldolase protein family. The encoded protein is a glycolytic enzyme that catalyzes the reversible conversion of fructose-1,6-bisphosphate to glyceraldehyde 3-phosphate and dihydroxyacetone phosphate. Three aldolase isozymes (A, B, and C), encoded by three different genes, are differentially expressed during development. Mutations in this gene have been associated with Glycogen Storage Disease XII, an autosomal recessive disorder associated with hemolytic anemia. Disruption of this gene also plays a role in the progression of multiple types of cancers. Related pseudogenes have been identified on chromosomes 3 and 10. [provided by RefSeq, Sep 2017]

LOC112694756 (HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ALDOA	NM_001243177.4	c.1200C>G	p.Ser400Arg	missense_variant	Exon 10 of 10	ENST00000642816.3	NP_001230106.1
LOC112694756	NM_001365304.2	c.*1547C>G		3_prime_UTR_variant	Exon 14 of 14	ENST00000338110.11	NP_001352233.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ALDOA	ENST00000642816.3	c.1200C>G	p.Ser400Arg	missense_variant	Exon 10 of 10		NM_001243177.4	ENSP00000496166.1
ENSG00000285043	ENST00000338110.11	c.*1547C>G		3_prime_UTR_variant	Exon 14 of 14	1	NM_001365304.2	ENSP00000336927.6

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.50
BayesDel_addAF	Uncertain	0.077	D
BayesDel_noAF	Benign	-0.13
CADD	Benign	3.5
DANN	Benign	0.90
DEOGEN2	Uncertain	0.77	.;D;D;D;D;.;D;.;.
Eigen	Benign	-0.98
Eigen_PC	Benign	-1.0
FATHMM_MKL	Benign	0.66	D
LIST_S2	Benign	0.72	T;.;.;.;.;.;T;T;.
M_CAP	Uncertain	0.17	D
MetaRNN	Uncertain	0.44	T;T;T;T;T;T;T;T;T
MetaSVM	Benign	-0.32	T
MutationAssessor	Pathogenic	3.1	.;M;M;M;M;.;M;.;.
PrimateAI	Uncertain	0.51	T
PROVEAN	Benign	-2.3	.;N;N;N;N;N;.;.;N
REVEL	Uncertain	0.47
Sift	Benign	0.094	.;T;T;T;T;T;.;.;T
Sift4G	Benign	0.15	T;T;T;T;T;T;.;.;T
Polyphen		0.0050	.;B;B;B;B;.;B;.;.
Vest4		0.39
MutPred		0.41		.;Loss of glycosylation at S346 (P = 0.0118);Loss of glycosylation at S346 (P = 0.0118);Loss of glycosylation at S346 (P = 0.0118);Loss of glycosylation at S346 (P = 0.0118);.;Loss of glycosylation at S346 (P = 0.0118);.;.;
MVP		0.75
ClinPred		0.20	T
GERP RS		-0.32
Varity_R		0.59
gMVP		0.45

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr16-30081476;