rs12666974

Variant summary

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

The NM_005000.5(NDUFA5):​c.67-1334A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.234 in 152,052 control chromosomes in the GnomAD database, including 4,801 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 0.23 ( 4801 hom., cov: 32)

Consequence

NDUFA5
NM_005000.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0640
Variant links:
Genes affected
NDUFA5 (HGNC:7688): (NADH:ubiquinone oxidoreductase subunit A5) This nuclear gene encodes a conserved protein that comprises the B13 subunit of complex I of the mitochondrial respiratory chain. The encoded protein localizes to the inner mitochondrial membrane, where it is thought to aid in the transfer of electrons from NADH to ubiquinone. Alternative splicing results in multiple transcript variants. There are numerous pseudogenes of this gene on chromosomes 1, 3, 6, 8, 9, 11, 12, and 16. [provided by RefSeq, Apr 2014]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.313 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
NDUFA5NM_005000.5 linkc.67-1334A>T intron_variant ENST00000355749.7 NP_004991.1 Q16718-1A0A024R745

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
NDUFA5ENST00000355749.7 linkc.67-1334A>T intron_variant 1 NM_005000.5 ENSP00000347988.2 Q16718-1

Frequencies

GnomAD3 genomes
AF:
0.234
AC:
35565
AN:
151934
Hom.:
4811
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.103
Gnomad AMI
AF:
0.275
Gnomad AMR
AF:
0.264
Gnomad ASJ
AF:
0.271
Gnomad EAS
AF:
0.327
Gnomad SAS
AF:
0.264
Gnomad FIN
AF:
0.407
Gnomad MID
AF:
0.142
Gnomad NFE
AF:
0.270
Gnomad OTH
AF:
0.218
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.234
AC:
35549
AN:
152052
Hom.:
4801
Cov.:
32
AF XY:
0.241
AC XY:
17869
AN XY:
74272
show subpopulations
Gnomad4 AFR
AF:
0.103
Gnomad4 AMR
AF:
0.264
Gnomad4 ASJ
AF:
0.271
Gnomad4 EAS
AF:
0.326
Gnomad4 SAS
AF:
0.263
Gnomad4 FIN
AF:
0.407
Gnomad4 NFE
AF:
0.270
Gnomad4 OTH
AF:
0.217
Alfa
AF:
0.253
Hom.:
806
Bravo
AF:
0.216
Asia WGS
AF:
0.280
AC:
973
AN:
3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
4.7
DANN
Benign
0.53

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: rs12666974; hg19: chr7-123191974; API