1-170159467-A-T

Position:

• chr1-170159467-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001136107.2(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 NM_001136107.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.364

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NTMT2	NM_001136107.2	c.155-1051A>T		intron_variant		ENST00000439373.3
NTMT2	XM_011509232.3	c.-41-1051A>T		intron_variant
NTMT2	XM_011509233.3	c.-41-1051A>T		intron_variant
NTMT2	XM_011509234.3	c.-41-1051A>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NTMT2	ENST00000439373.3	c.155-1051A>T		intron_variant		1	NM_001136107.2	P1
NTMT2	ENST00000367764.3	n.150-1051A>T		intron_variant, non_coding_transcript_variant		5

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

Gnomad4 AFR AF: 0.162

Gnomad4 AMR AF: 0.503

Gnomad4 ASJ AF: 0.508

Gnomad4 EAS AF: 0.701

Gnomad4 SAS AF: 0.509

Gnomad4 FIN AF: 0.521

Gnomad4 NFE AF: 0.480

Gnomad4 OTH AF: 0.458

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.71
DANN	Benign	0.75

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: rs495524; hg19: chr1-170128608;