6-143438600-T-C

Variant names:

• chr6-143438600-T-C
• rs2128741897
• NM_182503.3:c.191A>G

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_182503.3(ADAT2):​c.191A>G​(p.Gln64Arg) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as not provided (no stars).

• Frequency: Genomes: not found (cov: 32)
• Consequence: ADAT2 NM_182503.3 missense
• Clinical Significance: not provided no classification provided O:1
• Conservation: PhyloP100: 7.28
• Publications: 0 publications found

Genes affected

ADAT2 (HGNC:21172): (adenosine deaminase tRNA specific 2) Predicted to enable tRNA-specific adenosine-34 deaminase activity. Predicted to be involved in tRNA wobble adenosine to inosine editing. Predicted to be located in nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_182503.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADAT2	NM_182503.3	MANE Select	c.191A>G	p.Gln64Arg	missense	Exon 2 of 6	NP_872309.2	Q7Z6V5-1
	ADAT2	NM_001286259.2		c.50A>G	p.Gln17Arg	missense	Exon 2 of 6	NP_001273188.1	Q7Z6V5-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADAT2	ENST00000237283.9	TSL:1 MANE Select	c.191A>G	p.Gln64Arg	missense	Exon 2 of 6	ENSP00000237283.8	Q7Z6V5-1
	ADAT2	ENST00000606514.5	TSL:1	c.50A>G	p.Gln17Arg	missense	Exon 2 of 6	ENSP00000475651.1	Q7Z6V5-2
	ADAT2	ENST00000933835.1		c.97-4619A>G		intron	N/A	ENSP00000603894.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 32

ClinVar

ClinVar submissions

Significance: not provided

Revision: no classification provided

Pathogenic	VUS	Benign	Condition
-	-	-	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.10
BayesDel_addAF	Benign	-0.20	T
BayesDel_noAF	Benign	-0.53
CADD	Uncertain	26
DANN	Uncertain	0.99
DEOGEN2	Benign	0.078	T
Eigen	Benign	-0.095
Eigen_PC	Benign	0.16
FATHMM_MKL	Pathogenic	0.98	D
LIST_S2	Uncertain	0.89	D
M_CAP	Benign	0.0047	T
MetaRNN	Benign	0.21	T
MetaSVM	Benign	-1.1	T
MutationAssessor	Benign	-0.26	N
PhyloP100		7.3
PrimateAI	Uncertain	0.50	T
PROVEAN	Benign	-1.9	N
REVEL	Benign	0.078
Sift	Benign	0.18	T
Sift4G	Benign	0.23	T
Polyphen		0.0090	B
Vest4		0.24
MutPred		0.32		Loss of ubiquitination at K66 (P = 0.0246)
MVP		0.65
MPC		0.41
ClinPred		0.91	D
GERP RS		5.9
RBP_binding_hub_radar		0.92
RBP_regulation_power_radar		2.6
Varity_R		0.12
gMVP		0.79
Mutation Taster		=82/18	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.22		Details are displayed if max score is > 0.2
DS_DG_spliceai		0.22		Position offset: -14

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2128741897; hg19: chr6-143759737;