1-170159467-A-T

Variant names:

• chr1-170159467-A-T
• rs495524
• NM_001136107.2:c.155-1051A>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000439373.3(NTMT2):​c.155-1051A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.42 (12000 hom., cov: 19)
• Consequence: NTMT2 ENST00000439373.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.364
• Publications: 5 publications found

Genes affected

NTMT2 (HGNC:31932): (N-terminal Xaa-Pro-Lys N-methyltransferase 2) Enables N-terminal protein N-methyltransferase activity. Involved in N-terminal protein amino acid methylation. Located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.681 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000439373.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NTMT2	NM_001136107.2	MANE Select	c.155-1051A>T		intron	N/A	NP_001129579.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NTMT2	ENST00000439373.3	TSL:1 MANE Select	c.155-1051A>T		intron	N/A	ENSP00000408058.3
	NTMT2	ENST00000367764.3	TSL:5	n.150-1051A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.416 AC: 52613 AN: 126442 Hom.: 11997 Cov.: 19

Gnomad AFR AF: 0.162

Gnomad AMI AF: 0.584

Gnomad AMR AF: 0.503

Gnomad ASJ AF: 0.508

Gnomad EAS AF: 0.701

Gnomad SAS AF: 0.509

Gnomad FIN AF: 0.521

Gnomad MID AF: 0.518

Gnomad NFE AF: 0.480

Gnomad OTH AF: 0.454

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.416 AC: 52607 AN: 126472 Hom.: 12000 Cov.: 19 AF XY: 0.421 AC XY: 25234 AN XY: 59930

African (AFR) AF: 0.162 AC: 5033 AN: 31142

American (AMR) AF: 0.503 AC: 6000 AN: 11926

Ashkenazi Jewish (ASJ) AF: 0.508 AC: 1695 AN: 3334

East Asian (EAS) AF: 0.701 AC: 3204 AN: 4572

South Asian (SAS) AF: 0.509 AC: 2036 AN: 4002

European-Finnish (FIN) AF: 0.521 AC: 3054 AN: 5858

Middle Eastern (MID) AF: 0.505 AC: 101 AN: 200

European-Non Finnish (NFE) AF: 0.480 AC: 30209 AN: 62884

Other (OTH) AF: 0.458 AC: 787 AN: 1718

Alfa AF: 0.251 Hom.: 570

Bravo AF: 0.376

Asia WGS AF: 0.582 AC: 2018 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.71
DANN	Benign	0.75
PhyloP100		-0.36
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs495524; hg19: chr1-170128608;