NM_001349018.2:c.461-74T>A

Variant names:

• chr3-138306554-A-T
• rs9846480
• NM_001349018.2:c.461-74T>A

Variant summary

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

The NM_001349018.2(NME9):​c.461-74T>A 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: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: NME9 NM_001349018.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.205
• Publications: 21 publications found

Genes affected

NME9 (HGNC:21343): (NME/NM23 family member 9) Predicted to enable nucleoside diphosphate kinase activity. Predicted to be involved in nucleotide metabolic process. Predicted to be located in dynein axonemal particle. [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=-0.81).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001349018.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NME9	NM_001349018.2	MANE Select	c.461-74T>A		intron	N/A	NP_001335947.1	Q86XW9-1
	NME9	NM_001349024.2		c.344-74T>A		intron	N/A	NP_001335953.1
	NME9	NM_001349025.2		c.344-74T>A		intron	N/A	NP_001335954.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NME9	ENST00000333911.9	TSL:1 MANE Select	c.461-74T>A		intron	N/A	ENSP00000335444.3	Q86XW9-1
	NME9	ENST00000492993.5	TSL:1	n.278-74T>A		intron	N/A	ENSP00000419355.1	Q3KNW3
	NME9	ENST00000953094.1		c.461-74T>A		intron	N/A	ENSP00000623153.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 684506 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 361480

African (AFR) AF: 0.00 AC: 0 AN: 17702

American (AMR) AF: 0.00 AC: 0 AN: 33686

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 16920

East Asian (EAS) AF: 0.00 AC: 0 AN: 35860

South Asian (SAS) AF: 0.00 AC: 0 AN: 58824

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 49920

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3862

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 433764

Other (OTH) AF: 0.00 AC: 0 AN: 33968

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	6.6
DANN	Benign	0.64
PhyloP100		0.20

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs9846480; hg19: chr3-138025396;