rs1249698181

Variant names:

• chr10-87228628-G-A
• rs1249698181
• NM_001099338.2:c.748G>A

Your query was ambiguous. Multiple possible variants found:

• chr10-87228628-G-A
• chr10-87228628-G-C

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001099338.2(NUTM2A):​c.748G>A​(p.Ala250Thr) 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. 13/19 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 26)
• Consequence: NUTM2A NM_001099338.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.08

Genes affected

NUTM2A (HGNC:23438): (NUT family member 2A)

NUTM2A-AS1 (HGNC:45161): (NUTM2A antisense RNA 1)

ACMG classification

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=0.07111856).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NUTM2A	NM_001099338.2	c.748G>A	p.Ala250Thr	missense_variant	Exon 2 of 7	ENST00000381707.6	NP_001092808.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NUTM2A	ENST00000381707.6	c.748G>A	p.Ala250Thr	missense_variant	Exon 2 of 7	1	NM_001099338.2	ENSP00000371126.1

Frequencies

GnomAD3 genomes Cov.: 26

GnomAD4 exome Cov.: 28

GnomAD4 genome Cov.: 26

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.096
BayesDel_addAF	Benign	-0.22	T
BayesDel_noAF	Benign	-0.55
CADD	Benign	3.8
DANN	Benign	0.93
DEOGEN2	Benign	0.00053	T;.
Eigen	Benign	-0.91
Eigen_PC	Benign	-1.1
FATHMM_MKL	Benign	0.0026	N
LIST_S2	Benign	0.61	T;T
M_CAP	Benign	0.0019	T
MetaRNN	Benign	0.071	T;T
MetaSVM	Benign	-1.0	T
PrimateAI	Uncertain	0.59	T
PROVEAN	Benign	0.36	N;N
REVEL	Benign	0.033
Sift	Benign	1.0	T;T
Sift4G	Benign	0.54	T;T
Polyphen		0.33	B;.
Vest4		0.15
MutPred		0.38		Gain of glycosylation at A250 (P = 0.0017);Gain of glycosylation at A250 (P = 0.0017);
MVP		0.34
ClinPred		0.17	T
GERP RS		-1.6
Varity_R		0.033
gMVP		0.035

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: rs1249698181; hg19: chr10-88988385; COSMIC: COSV101095742;