rs962888

chr17-44981703-G-A

Variant summary

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

The ENST00000690201.1(ENSG00000289024):n.226-3903G>A 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 0.359 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: ENST00000690201.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.77

Genes affected

(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=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.483 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000690201.1	n.226-3903G>A		intron_variant, non_coding_transcript_variant
NMT1	ENST00000678938.1	c.-110+23641G>A		intron_variant

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

Gnomad4 AFR AF: 0.488

Gnomad4 AMR AF: 0.288

Gnomad4 ASJ AF: 0.305

Gnomad4 EAS AF: 0.344

Gnomad4 SAS AF: 0.486

Gnomad4 FIN AF: 0.311

Gnomad4 NFE AF: 0.302

Gnomad4 OTH AF: 0.321

Alfa AF: 0.332 Hom.: 5479

Bravo AF: 0.357

Asia WGS AF: 0.403 AC: 1403 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	0.31
Dann	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs962888; hg19: chr17-43059071;