17-74773195-T-G

Variant names:

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

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_015654.5(NAT9):​c.191-156A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 31)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).

Transcripts

RefSeq

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

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 815064 Hom.: 0 Cov.: 11 AF XY: 0.00 AC XY: 0 AN XY: 409790

African (AFR) AF: 0.00 AC: 0 AN: 18982

American (AMR) AF: 0.00 AC: 0 AN: 19162

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 16078

East Asian (EAS) AF: 0.00 AC: 0 AN: 32696

South Asian (SAS) AF: 0.00 AC: 0 AN: 52406

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 30044

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2740

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 604796

Other (OTH) AF: 0.00 AC: 0 AN: 38160

GnomAD4 genome Cov.: 31

Alfa AF: 0.00 Hom.: 6944

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.47
DANN	Benign	0.73
PhyloP100		-0.62
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

Other links and lift over

dbSNP: rs878906; hg19: chr17-72769334;