rs900164167

Variant names:

• chr7-55964655-G-A
• rs900164167
• NM_001483.3:c.46G>A

Your query was ambiguous. Multiple possible variants found:

• chr7-55964655-G-A
• chr7-55964655-G-C
• chr7-55964655-G-T

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001483.3(NIPSNAP2):​c.46G>A​(p.Gly16Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000105 in 955,882 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/22 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G16C) has been classified as Uncertain significance.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0000010 (0 hom.)
• Consequence: NIPSNAP2 NM_001483.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.94
• Publications: 0 publications found

Genes affected

NIPSNAP2 (HGNC:4179): (nipsnap homolog 2) This gene encodes a member of the NipSnap family of proteins that may be involved in vesicular transport. The encoded protein is localized to mitochondria and plays a role in oxidative phosphorylation. A pseudogene of this gene is located on the long arm of chromosome 2. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Feb 2011]

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.11057976).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001483.3. 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
	NIPSNAP2	NM_001483.3	MANE Select	c.46G>A	p.Gly16Ser	missense	Exon 1 of 10	NP_001474.1	O75323-1
	NIPSNAP2	NM_001202469.2		c.46G>A	p.Gly16Ser	missense	Exon 1 of 8	NP_001189398.1	O75323-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NIPSNAP2	ENST00000322090.8	TSL:1 MANE Select	c.46G>A	p.Gly16Ser	missense	Exon 1 of 10	ENSP00000313050.3	O75323-1
	NIPSNAP2	ENST00000878201.1		c.46G>A	p.Gly16Ser	missense	Exon 1 of 11	ENSP00000548260.1
	NIPSNAP2	ENST00000878203.1		c.46G>A	p.Gly16Ser	missense	Exon 1 of 10	ENSP00000548262.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000105 AC: 1 AN: 955882 Hom.: 0 Cov.: 29 AF XY: 0.00000223 AC XY: 1 AN XY: 448706

African (AFR) AF: 0.00 AC: 0 AN: 18826

American (AMR) AF: 0.00 AC: 0 AN: 4558

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 9146

East Asian (EAS) AF: 0.00 AC: 0 AN: 14208

South Asian (SAS) AF: 0.00 AC: 0 AN: 18346

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 12838

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2268

European-Non Finnish (NFE) AF: 0.00000119 AC: 1 AN: 840766

Other (OTH) AF: 0.00 AC: 0 AN: 34926

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.13
BayesDel_addAF	Benign	-0.12	T
BayesDel_noAF	Benign	-0.41
CADD	Benign	18
DANN	Benign	0.96
DEOGEN2	Benign	0.013	T
Eigen	Benign	-0.90
Eigen_PC	Benign	-0.90
FATHMM_MKL	Benign	0.087	N
LIST_S2	Benign	0.61	T
M_CAP	Benign	0.065	D
MetaRNN	Benign	0.11	T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	0.0	N
PhyloP100		1.9
PrimateAI	Pathogenic	0.82	D
PROVEAN	Benign	0.55	N
REVEL	Benign	0.064
Sift	Benign	0.37	T
Sift4G	Benign	0.60	T
Polyphen		0.046	B
Vest4		0.28
MutPred		0.31		Loss of catalytic residue at G16 (P = 0.0094)
MVP		0.42
MPC		0.44
ClinPred		0.078	T
GERP RS		1.9
PromoterAI		-0.12	Neutral
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		2.1
Varity_R		0.056
gMVP		0.45
Mutation Taster		=99/1	polymorphism

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: rs900164167; hg19: chr7-56032348;