1-169164383-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_013330.5(NME7):​c.1098+5064G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0438 in 152,220 control chromosomes in the GnomAD database, including 218 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 0.044 ( 218 hom., cov: 32)

Consequence

NME7
NM_013330.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.88
Variant links:
Genes affected
NME7 (HGNC:20461): (NME/NM23 family member 7) This gene encodes a member of the non-metastatic expressed family of nucleoside diphosphate kinases. Members of this family are enzymes that catalyzes phosphate transfer from nucleoside triphosphates to nucleoside diphosphates. This protein contains two kinase domains, one of which is involved in autophosphorylation and the other may be inactive. This protein localizes to the centrosome and functions as a component of the gamma-tubulin ring complex which plays a role in microtubule organization. Mutations in this gene may be associated with venous thromboembolism. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Sep 2016]
ATP1B1 (HGNC:804): (ATPase Na+/K+ transporting subunit beta 1) The protein encoded by this gene belongs to the family of Na+/K+ and H+/K+ ATPases beta chain proteins, and to the subfamily of Na+/K+ -ATPases. Na+/K+ -ATPase is an integral membrane protein responsible for establishing and maintaining the electrochemical gradients of Na and K ions across the plasma membrane. These gradients are essential for osmoregulation, for sodium-coupled transport of a variety of organic and inorganic molecules, and for electrical excitability of nerve and muscle. This enzyme is composed of two subunits, a large catalytic subunit (alpha) and a smaller glycoprotein subunit (beta). The beta subunit regulates, through assembly of alpha/beta heterodimers, the number of sodium pumps transported to the plasma membrane. The glycoprotein subunit of Na+/K+ -ATPase is encoded by multiple genes. This gene encodes a beta 1 subunit. Alternatively spliced transcript variants encoding different isoforms have been described, but their biological validity is not known. [provided by RefSeq, Mar 2010]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.94).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.125 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
NME7NM_013330.5 linkuse as main transcriptc.1098+5064G>A intron_variant ENST00000367811.8 NP_037462.1
NME7NM_197972.3 linkuse as main transcriptc.990+5064G>A intron_variant NP_932076.1
NME7NR_104229.2 linkuse as main transcriptn.1248+5064G>A intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
NME7ENST00000367811.8 linkuse as main transcriptc.1098+5064G>A intron_variant 1 NM_013330.5 ENSP00000356785 P1Q9Y5B8-1

Frequencies

GnomAD3 genomes
AF:
0.0438
AC:
6663
AN:
152112
Hom.:
218
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0312
Gnomad AMI
AF:
0.0319
Gnomad AMR
AF:
0.0468
Gnomad ASJ
AF:
0.111
Gnomad EAS
AF:
0.133
Gnomad SAS
AF:
0.0786
Gnomad FIN
AF:
0.00509
Gnomad MID
AF:
0.0860
Gnomad NFE
AF:
0.0439
Gnomad OTH
AF:
0.0488
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0438
AC:
6668
AN:
152220
Hom.:
218
Cov.:
32
AF XY:
0.0440
AC XY:
3271
AN XY:
74418
show subpopulations
Gnomad4 AFR
AF:
0.0314
Gnomad4 AMR
AF:
0.0467
Gnomad4 ASJ
AF:
0.111
Gnomad4 EAS
AF:
0.133
Gnomad4 SAS
AF:
0.0785
Gnomad4 FIN
AF:
0.00509
Gnomad4 NFE
AF:
0.0439
Gnomad4 OTH
AF:
0.0502
Alfa
AF:
0.0475
Hom.:
233
Bravo
AF:
0.0456
Asia WGS
AF:
0.0950
AC:
329
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.94
CADD
Benign
0.074
DANN
Benign
0.43

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs12074013; hg19: chr1-169133621; API