NM_001330449.2:c.250A>G

Variant names:

• chr16-2521013-A-G
• rs912444016
• NM_001330449.2:c.250A>G

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001330449.2(AMDHD2):​c.250A>G​(p.Thr84Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T84S) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: AMDHD2 NM_001330449.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.176

Genes affected

AMDHD2 (HGNC:24262): (amidohydrolase domain containing 2) Enables N-acetylglucosamine-6-phosphate deacetylase activity. Predicted to be involved in N-acetylglucosamine catabolic process. Located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000259784 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.05563283).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AMDHD2	NM_001330449.2	c.250A>G	p.Thr84Ala	missense_variant	Exon 3 of 11	ENST00000293971.11	NP_001317378.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AMDHD2	ENST00000293971.11	c.250A>G	p.Thr84Ala	missense_variant	Exon 3 of 11	1	NM_001330449.2	ENSP00000293971.6
ENSG00000259784	ENST00000569317.1	c.109A>G	p.Thr37Ala	missense_variant	Exon 2 of 4	3		ENSP00000455561.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 32

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.067
BayesDel_addAF	Benign	-0.23	T
BayesDel_noAF	Benign	-0.57
CADD	Benign	13
DANN	Benign	0.75
DEOGEN2	Benign	0.21	.;T;.;.;.;.;T;T
Eigen	Benign	-0.82
Eigen_PC	Benign	-0.77
FATHMM_MKL	Uncertain	0.86	D
LIST_S2	Benign	0.71	T;T;T;T;T;T;T;T
M_CAP	Benign	0.0052	T
MetaRNN	Benign	0.056	T;T;T;T;T;T;T;T
MetaSVM	Benign	-0.95	T
MutationAssessor	Benign	1.8	.;L;L;L;.;.;.;.
PrimateAI	Benign	0.44	T
PROVEAN	Benign	-0.85	N;N;N;N;.;N;N;N
REVEL	Benign	0.015
Sift	Benign	0.30	T;T;T;T;.;T;T;T
Sift4G	Benign	0.25	T;T;T;T;.;T;T;T
Polyphen		0.0, 0.011	.;B;B;B;.;.;.;.
Vest4		0.23, 0.27, 0.28
MutPred		0.40		.;Gain of loop (P = 0.0851);Gain of loop (P = 0.0851);Gain of loop (P = 0.0851);Gain of loop (P = 0.0851);Gain of loop (P = 0.0851);Gain of loop (P = 0.0851);Gain of loop (P = 0.0851);
MVP		0.048
MPC		0.67
ClinPred		0.057	T
GERP RS		1.6
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Varity_R		0.085
gMVP		0.46

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

Other links and lift over

dbSNP: rs912444016; hg19: chr16-2571014;