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GeneBe

16-23587263-C-T

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_005003.3(NDUFAB1):c.225G>A(p.Thr75=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00405 in 1,613,996 control chromosomes in the GnomAD database, including 30 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0026 ( 2 hom., cov: 33)
Exomes 𝑓: 0.0042 ( 28 hom. )

Consequence

NDUFAB1
NM_005003.3 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -2.09
Variant links:
Genes affected
NDUFAB1 (HGNC:7694): (NADH:ubiquinone oxidoreductase subunit AB1) Predicted to enable acyl binding activity; acyl carrier activity; and fatty acid binding activity. Involved in mitochondrial respiratory chain complex I assembly and protein lipoylation. Located in mitochondrion and nucleoplasm. Part of mitochondrial respiratory chain complex I. Colocalizes with mitochondrial large ribosomal subunit. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.66).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 16-23587263-C-T is Benign according to our data. Variant chr16-23587263-C-T is described in ClinVar as [Benign]. Clinvar id is 718238.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=-2.09 with no splicing effect.
BS2
?
    BS2 - Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age
High Homozygotes in GnomAd at 2 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
NDUFAB1NM_005003.3 linkuse as main transcriptc.225G>A p.Thr75= synonymous_variant 2/5 ENST00000007516.8
NDUFAB1XM_011545856.3 linkuse as main transcriptc.318G>A p.Thr106= synonymous_variant 3/6

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
NDUFAB1ENST00000007516.8 linkuse as main transcriptc.225G>A p.Thr75= synonymous_variant 2/51 NM_005003.3 P1

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00266
AC:
404
AN:
152158
Hom.:
2
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.00113
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000916
Gnomad ASJ
AF:
0.00375
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00104
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00466
Gnomad OTH
AF:
0.000955
GnomAD3 exomes
AF:
0.00313
AC:
788
AN:
251458
Hom.:
3
AF XY:
0.00303
AC XY:
412
AN XY:
135914
show subpopulations
Gnomad AFR exome
AF:
0.00135
Gnomad AMR exome
AF:
0.000549
Gnomad ASJ exome
AF:
0.00456
Gnomad EAS exome
AF:
0.0000544
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.000924
Gnomad NFE exome
AF:
0.00581
Gnomad OTH exome
AF:
0.00310
GnomAD4 exome
AF:
0.00420
AC:
6141
AN:
1461720
Hom.:
28
Cov.:
30
AF XY:
0.00403
AC XY:
2930
AN XY:
727178
show subpopulations
Gnomad4 AFR exome
AF:
0.000627
Gnomad4 AMR exome
AF:
0.000447
Gnomad4 ASJ exome
AF:
0.00528
Gnomad4 EAS exome
AF:
0.0000252
Gnomad4 SAS exome
AF:
0.0000464
Gnomad4 FIN exome
AF:
0.00109
Gnomad4 NFE exome
AF:
0.00515
Gnomad4 OTH exome
AF:
0.00293
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00265
AC:
403
AN:
152276
Hom.:
2
Cov.:
33
AF XY:
0.00261
AC XY:
194
AN XY:
74452
show subpopulations
Gnomad4 AFR
AF:
0.00113
Gnomad4 AMR
AF:
0.000915
Gnomad4 ASJ
AF:
0.00375
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00104
Gnomad4 NFE
AF:
0.00465
Gnomad4 OTH
AF:
0.000945
Alfa
AF:
0.00422
Hom.:
0
Bravo
AF:
0.00249
Asia WGS
AF:
0.000577
AC:
2
AN:
3478
EpiCase
AF:
0.00354
EpiControl
AF:
0.00433

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingInvitaeApr 02, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.66
Cadd
Benign
6.8
Dann
Benign
0.58
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7

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: rs139679834; hg19: chr16-23598584; API