chr17-44981703-G-A

Variant names:

• chr17-44981703-G-A
• rs962888

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 0.359 in 152,076 control chromosomes in the GnomAD database, including 10,503 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 0.36 (10503 hom., cov: 32)
• Consequence: LOC112268183 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.77
• Publications: 17 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=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.483 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+23641G>A		intron	N/A	ENSP00000503621.1
	ENSG00000289024	ENST00000690201.2		n.330-3903G>A		intron	N/A
	ENSG00000294432	ENST00000723577.1		n.272-459C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.359 AC: 54599 AN: 151958 Hom.: 10480 Cov.: 32

Gnomad AFR AF: 0.488

Gnomad AMI AF: 0.231

Gnomad AMR AF: 0.288

Gnomad ASJ AF: 0.305

Gnomad EAS AF: 0.342

Gnomad SAS AF: 0.486

Gnomad FIN AF: 0.311

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.302

Gnomad OTH AF: 0.324

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

GnomAD4 genome AF: 0.359 AC: 54663 AN: 152076 Hom.: 10503 Cov.: 32 AF XY: 0.359 AC XY: 26690 AN XY: 74316

African (AFR) AF: 0.488 AC: 20248 AN: 41450

American (AMR) AF: 0.288 AC: 4403 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.305 AC: 1059 AN: 3470

East Asian (EAS) AF: 0.344 AC: 1779 AN: 5178

South Asian (SAS) AF: 0.486 AC: 2348 AN: 4828

European-Finnish (FIN) AF: 0.311 AC: 3282 AN: 10566

Middle Eastern (MID) AF: 0.344 AC: 101 AN: 294

European-Non Finnish (NFE) AF: 0.302 AC: 20556 AN: 67990

Other (OTH) AF: 0.321 AC: 677 AN: 2106

Alfa AF: 0.348 Hom.: 10490

Bravo AF: 0.357

Asia WGS AF: 0.403 AC: 1403 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.31
DANN	Benign	0.66
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs962888; hg19: chr17-43059071;