17-74773195-T-C

Variant names:

• chr17-74773195-T-C
• rs878906
• NM_015654.5:c.191-156A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
NAT9	NM_015654.5	c.191-156A>G		intron_variant	Intron 3 of 6	ENST00000357814.8	NP_056469.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NAT9	ENST00000357814.8	c.191-156A>G		intron_variant	Intron 3 of 6	1	NM_015654.5	ENSP00000350467.3

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

African (AFR) AF: 0.477 AC: 9034 AN: 18930

American (AMR) AF: 0.559 AC: 10692 AN: 19140

Ashkenazi Jewish (ASJ) AF: 0.488 AC: 7841 AN: 16056

East Asian (EAS) AF: 0.309 AC: 10090 AN: 32662

South Asian (SAS) AF: 0.449 AC: 23513 AN: 52320

European-Finnish (FIN) AF: 0.547 AC: 16404 AN: 30006

Middle Eastern (MID) AF: 0.417 AC: 1142 AN: 2740

European-Non Finnish (NFE) AF: 0.530 AC: 319345 AN: 602854

Other (OTH) AF: 0.499 AC: 18976 AN: 38066

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

African (AFR) AF: 0.479 AC: 19834 AN: 41382

American (AMR) AF: 0.521 AC: 7955 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.500 AC: 1732 AN: 3462

East Asian (EAS) AF: 0.309 AC: 1599 AN: 5168

South Asian (SAS) AF: 0.441 AC: 2120 AN: 4802

European-Finnish (FIN) AF: 0.554 AC: 5841 AN: 10546

Middle Eastern (MID) AF: 0.459 AC: 135 AN: 294

European-Non Finnish (NFE) AF: 0.527 AC: 35769 AN: 67922

Other (OTH) AF: 0.488 AC: 1031 AN: 2114

Alfa AF: 0.515 Hom.: 6944

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
PhyloP100		-0.62
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.2
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs878906; hg19: chr17-72769334;