rs878906

Positions:

• chr17-74773195-T-C
• chr17-74773195-T-G

Variant summary

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

The NM_015654.5(NAT9):​c.191-156A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.511 in 964,648 control chromosomes in the GnomAD database, including 127,584 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 0.50 (19401 hom., cov: 31)
  • Exomes 𝑓: 0.51 (108183 hom.)
• Consequence: NAT9 NM_015654.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.617

Genes affected

NAT9 (HGNC:23133): (N-acetyltransferase 9 (putative)) Predicted to enable N-acetyltransferase activity. Predicted to be involved in protein acetylation. Part of protein-containing complex. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.522 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NAT9	NM_015654.5	c.191-156A>G		intron_variant		ENST00000357814.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NAT9	ENST00000357814.8	c.191-156A>G		intron_variant		1	NM_015654.5	P4

Frequencies

GnomAD3 genomes AF: 0.502 AC: 76204 AN: 151754 Hom.: 19352 Cov.: 31

Gnomad AFR AF: 0.479

Gnomad AMI AF: 0.318

Gnomad AMR AF: 0.520

Gnomad ASJ AF: 0.500

Gnomad EAS AF: 0.309

Gnomad SAS AF: 0.442

Gnomad FIN AF: 0.554

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.527

Gnomad OTH AF: 0.483

GnomAD4 exome AF: 0.513 AC: 417037 AN: 812774 Hom.: 108183 Cov.: 11 AF XY: 0.510 AC XY: 208586 AN XY: 408736

Gnomad4 AFR exome AF: 0.477

Gnomad4 AMR exome AF: 0.559

Gnomad4 ASJ exome AF: 0.488

Gnomad4 EAS exome AF: 0.309

Gnomad4 SAS exome AF: 0.449

Gnomad4 FIN exome AF: 0.547

Gnomad4 NFE exome AF: 0.530

Gnomad4 OTH exome AF: 0.499

GnomAD4 genome AF: 0.502 AC: 76306 AN: 151874 Hom.: 19401 Cov.: 31 AF XY: 0.503 AC XY: 37344 AN XY: 74238

Gnomad4 AFR AF: 0.479

Gnomad4 AMR AF: 0.521

Gnomad4 ASJ AF: 0.500

Gnomad4 EAS AF: 0.309

Gnomad4 SAS AF: 0.441

Gnomad4 FIN AF: 0.554

Gnomad4 NFE AF: 0.527

Gnomad4 OTH AF: 0.488

Alfa AF: 0.520 Hom.: 4129

Bravo AF: 0.502

Asia WGS AF: 0.384 AC: 1338 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.53
DANN	Benign	0.69
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.2

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs878906; hg19: chr17-72769334;