rs17547180

Variant names:

• chr17-44974024-C-A
• rs17547180

Variant summary

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

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: LOC112268183 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.492
• Publications: 6 publications found

Genes affected

LOC112268183 (HGNC:):

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000678938.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NMT1	ENST00000678938.1		c.-110+15962C>A		intron	N/A	ENSP00000503621.1

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

African (AFR) AF: 0.0137 AC: 569 AN: 41564

American (AMR) AF: 0.0567 AC: 867 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.119 AC: 412 AN: 3472

East Asian (EAS) AF: 0.000579 AC: 3 AN: 5184

South Asian (SAS) AF: 0.0170 AC: 82 AN: 4832

European-Finnish (FIN) AF: 0.0711 AC: 754 AN: 10604

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.0747 AC: 5084 AN: 68022

Other (OTH) AF: 0.0516 AC: 109 AN: 2114

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	6.4
DANN	Benign	0.76
PhyloP100		-0.49

Splicing

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

Other links and lift over

dbSNP: rs17547180; hg19: chr17-43051392;