rs17547180

chr17-44974024-C-A

Variant summary

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

The ENST00000678938.1(NMT1):c.-110+15962C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0521 in 152,296 control chromosomes in the GnomAD database, including 310 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 0.052 (310 hom., cov: 31)
• Consequence: NMT1 ENST00000678938.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.492

Genes affected

NMT1 (HGNC:7857): (N-myristoyltransferase 1) Myristate, a rare 14-carbon saturated fatty acid, is cotranslationally attached by an amide linkage to the N-terminal glycine residue of cellular and viral proteins with diverse functions. N-myristoyltransferase (NMT; EC 2.3.1.97) catalyzes the transfer of myristate from CoA to proteins. N-myristoylation appears to be irreversible and is required for full expression of the biologic activities of several N-myristoylated proteins, including the alpha subunit of the signal-transducing guanine nucleotide-binding protein (G protein) GO (GNAO1; MIM 139311) (Duronio et al., 1992 [PubMed 1570339]).[supplied by OMIM, Nov 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.073 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NMT1	ENST00000678938.1	c.-110+15962C>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.0521 AC: 7932 AN: 152178 Hom.: 310 Cov.: 31

Gnomad AFR AF: 0.0137

Gnomad AMI AF: 0.0318

Gnomad AMR AF: 0.0568

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0163

Gnomad FIN AF: 0.0711

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0747

Gnomad OTH AF: 0.0516

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

GnomAD4 genome AF: 0.0521 AC: 7932 AN: 152296 Hom.: 310 Cov.: 31 AF XY: 0.0518 AC XY: 3858 AN XY: 74468

Gnomad4 AFR AF: 0.0137

Gnomad4 AMR AF: 0.0567

Gnomad4 ASJ AF: 0.119

Gnomad4 EAS AF: 0.000579

Gnomad4 SAS AF: 0.0170

Gnomad4 FIN AF: 0.0711

Gnomad4 NFE AF: 0.0747

Gnomad4 OTH AF: 0.0516

Alfa AF: 0.0624 Hom.: 91

Bravo AF: 0.0509

Asia WGS AF: 0.0100 AC: 37 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	6.4
Dann	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17547180; hg19: chr17-43051392;