rs4735339

Variant summary

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

The NM_001354516.2(NDUFAF6):​c.-79+3966C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.507 in 152,008 control chromosomes in the GnomAD database, including 19,927 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 0.51 ( 19927 hom., cov: 33)

Consequence

NDUFAF6
NM_001354516.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0760
Variant links:
Genes affected
NDUFAF6 (HGNC:28625): (NADH:ubiquinone oxidoreductase complex assembly factor 6) This gene encodes a protein that localizes to mitochondria and contains a predicted phytoene synthase domain. The encoded protein plays an important role in the assembly of complex I (NADH-ubiquinone oxidoreductase) of the mitochondrial respiratory chain through regulation of subunit ND1 biogenesis. Mutations in this gene are associated with complex I enzymatic deficiency. [provided by RefSeq, Nov 2011]

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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=-0.8).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.703 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
NDUFAF6NM_001354514.2 linkuse as main transcriptc.-301+3966C>T intron_variant
NDUFAF6NM_001354515.2 linkuse as main transcriptc.-84+3966C>T intron_variant
NDUFAF6NM_001354516.2 linkuse as main transcriptc.-79+3966C>T intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
NDUFAF6ENST00000396111.6 linkuse as main transcriptc.-199+3966C>T intron_variant 5
NDUFAF6ENST00000396113.5 linkuse as main transcriptc.-614+3966C>T intron_variant 5
NDUFAF6ENST00000519136.5 linkuse as main transcriptc.-256+3966C>T intron_variant 5

Frequencies

GnomAD3 genomes
AF:
0.507
AC:
76962
AN:
151890
Hom.:
19916
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.412
Gnomad AMI
AF:
0.543
Gnomad AMR
AF:
0.562
Gnomad ASJ
AF:
0.507
Gnomad EAS
AF:
0.723
Gnomad SAS
AF:
0.583
Gnomad FIN
AF:
0.561
Gnomad MID
AF:
0.475
Gnomad NFE
AF:
0.520
Gnomad OTH
AF:
0.530
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.507
AC:
77015
AN:
152008
Hom.:
19927
Cov.:
33
AF XY:
0.513
AC XY:
38131
AN XY:
74282
show subpopulations
Gnomad4 AFR
AF:
0.412
Gnomad4 AMR
AF:
0.562
Gnomad4 ASJ
AF:
0.507
Gnomad4 EAS
AF:
0.722
Gnomad4 SAS
AF:
0.584
Gnomad4 FIN
AF:
0.561
Gnomad4 NFE
AF:
0.520
Gnomad4 OTH
AF:
0.531
Alfa
AF:
0.499
Hom.:
3088
Bravo
AF:
0.504
Asia WGS
AF:
0.595
AC:
2066
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.80
CADD
Benign
8.6
DANN
Benign
0.80

Splicing

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: rs4735339; hg19: chr8-95974373; API