rs6703198

Variant names:

• chr1-170147101-T-C
• rs6703198
• NM_001136107.2:c.154+840T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NM_001136107.2(NTMT2):​c.154+840T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0274 in 152,304 control chromosomes in the GnomAD database, including 83 homozygotes. 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 0.027 (83 hom., cov: 32)
• Consequence: NTMT2 NM_001136107.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.979
• Publications: 1 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).
• BS1: Variant frequency is greater than expected in population sas. GnomAd4 allele frequency = 0.0274 (4175/152304) while in subpopulation SAS AF = 0.0454 (219/4826). AF 95% confidence interval is 0.0405. There are 83 homozygotes in GnomAd4. There are 1903 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 83 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001136107.2. 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.154+840T>C		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.154+840T>C		intron	N/A	ENSP00000408058.3

Frequencies

GnomAD3 genomes AF: 0.0274 AC: 4172 AN: 152186 Hom.: 83 Cov.: 32

Gnomad AFR AF: 0.00832

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0164

Gnomad ASJ AF: 0.0262

Gnomad EAS AF: 0.00983

Gnomad SAS AF: 0.0451

Gnomad FIN AF: 0.0302

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0418

Gnomad OTH AF: 0.0253

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

GnomAD4 genome AF: 0.0274 AC: 4175 AN: 152304 Hom.: 83 Cov.: 32 AF XY: 0.0255 AC XY: 1903 AN XY: 74486

African (AFR) AF: 0.00832 AC: 346 AN: 41584

American (AMR) AF: 0.0163 AC: 250 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0262 AC: 91 AN: 3470

East Asian (EAS) AF: 0.00985 AC: 51 AN: 5178

South Asian (SAS) AF: 0.0454 AC: 219 AN: 4826

European-Finnish (FIN) AF: 0.0302 AC: 320 AN: 10604

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.0418 AC: 2840 AN: 68016

Other (OTH) AF: 0.0255 AC: 54 AN: 2116

Alfa AF: 0.0390 Hom.: 57

Bravo AF: 0.0246

Asia WGS AF: 0.0410 AC: 144 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.23
DANN	Benign	0.21
PhyloP100		-0.98
Mutation Taster		=100/0	polymorphism

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: rs6703198; hg19: chr1-170116242;