rs4792963

Variant names:

• chr17-44994244-A-G
• rs4792963
• ENST00000678938.1:c.-110+36182A>G

Your query was ambiguous. Multiple possible variants found:

• chr17-44994244-A-G
• chr17-44994244-A-T

Variant summary

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

The ENST00000678938.1(NMT1):​c.-110+36182A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.224 in 152,122 control chromosomes in the GnomAD database, including 5,061 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 0.22 (5061 hom., cov: 32)
• Consequence: NMT1 ENST00000678938.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.316
• Publications: 0 publications found

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]

ENSG00000294432 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.408 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NMT1	ENST00000678938.1		c.-110+36182A>G		intron	N/A	ENSP00000503621.1	P30419-2
	ENSG00000294432	ENST00000723575.1		n.545+2122T>C		intron	N/A
	ENSG00000294432	ENST00000723576.1		n.269-2079T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.224 AC: 34034 AN: 152004 Hom.: 5042 Cov.: 32

Gnomad AFR AF: 0.412

Gnomad AMI AF: 0.0230

Gnomad AMR AF: 0.263

Gnomad ASJ AF: 0.145

Gnomad EAS AF: 0.267

Gnomad SAS AF: 0.219

Gnomad FIN AF: 0.153

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.116

Gnomad OTH AF: 0.225

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

GnomAD4 genome AF: 0.224 AC: 34099 AN: 152122 Hom.: 5061 Cov.: 32 AF XY: 0.226 AC XY: 16827 AN XY: 74376

African (AFR) AF: 0.413 AC: 17114 AN: 41468

American (AMR) AF: 0.263 AC: 4027 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.145 AC: 504 AN: 3470

East Asian (EAS) AF: 0.266 AC: 1375 AN: 5162

South Asian (SAS) AF: 0.218 AC: 1050 AN: 4822

European-Finnish (FIN) AF: 0.153 AC: 1619 AN: 10598

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.116 AC: 7860 AN: 68000

Other (OTH) AF: 0.225 AC: 475 AN: 2110

Alfa AF: 0.129 Hom.: 880

Bravo AF: 0.244

Asia WGS AF: 0.281 AC: 978 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.4
DANN	Benign	0.70
PhyloP100		0.32

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4792963;

hg19: chr17-43071612;