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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107987243	XR_007065771.1	n.951-2079T>C		intron_variant	Intron 4 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NMT1	ENST00000678938.1	c.-110+36182A>G		intron_variant	Intron 1 of 11			ENSP00000503621.1
ENSG00000294432	ENST00000723575.1	n.545+2122T>C		intron_variant	Intron 4 of 5
ENSG00000294432	ENST00000723576.1	n.269-2079T>C		intron_variant	Intron 2 of 4

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 v4.3

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

Other links and lift over

dbSNP: rs4792963; hg19: chr17-43071612;