rs4792963

Positions:

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

Variant summary

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

The XR_007065771.1(LOC107987243):​n.951-2079T>C variant causes a intron, non coding transcript 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: LOC107987243 XR_007065771.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.316

Genes affected

LOC107987243 (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

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
LOC107987243	XR_007065771.1	n.951-2079T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NMT1	ENST00000678938.1	c.-110+36182A>G		intron_variant				ENSP00000503621

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

Gnomad4 AFR AF: 0.413

Gnomad4 AMR AF: 0.263

Gnomad4 ASJ AF: 0.145

Gnomad4 EAS AF: 0.266

Gnomad4 SAS AF: 0.218

Gnomad4 FIN AF: 0.153

Gnomad4 NFE AF: 0.116

Gnomad4 OTH AF: 0.225

Alfa AF: 0.126 Hom.: 724

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4792963; hg19: chr17-43071612;