chr19-8311547-G-A

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_005001.5(NDUFA7):​c.300C>T​(p.Pro100Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.179 in 1,611,872 control chromosomes in the GnomAD database, including 27,727 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 0.16 ( 2232 hom., cov: 32)
Exomes 𝑓: 0.18 ( 25495 hom. )

Consequence

NDUFA7
NM_005001.5 synonymous

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.33

Publications

30 publications found
Variant links:
Genes affected
NDUFA7 (HGNC:7691): (NADH:ubiquinone oxidoreductase subunit A7) This gene encodes a subunit of NADH:ubiquinone oxidoreductase (complex I), which is a multiprotein complex located in the inner mitochondrial membrane. Complex I functions in the transfer of electrons from NADH to the respiratory chain. [provided by RefSeq, Mar 2011]

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -13 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.66).
BP7
Synonymous conserved (PhyloP=-1.33 with no splicing effect.
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.251 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
NDUFA7NM_005001.5 linkc.300C>T p.Pro100Pro synonymous_variant Exon 4 of 4 ENST00000301457.3 NP_004992.2 O95182
NDUFA7NR_135539.2 linkn.317C>T non_coding_transcript_exon_variant Exon 4 of 5

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
NDUFA7ENST00000301457.3 linkc.300C>T p.Pro100Pro synonymous_variant Exon 4 of 4 1 NM_005001.5 ENSP00000301457.1 O95182
ENSG00000167774ENST00000598884.1 linkn.300C>T non_coding_transcript_exon_variant Exon 4 of 5 4 ENSP00000470609.1

Frequencies

GnomAD3 genomes
AF:
0.156
AC:
23679
AN:
152066
Hom.:
2233
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0511
Gnomad AMI
AF:
0.219
Gnomad AMR
AF:
0.258
Gnomad ASJ
AF:
0.196
Gnomad EAS
AF:
0.218
Gnomad SAS
AF:
0.0758
Gnomad FIN
AF:
0.183
Gnomad MID
AF:
0.206
Gnomad NFE
AF:
0.189
Gnomad OTH
AF:
0.195
GnomAD2 exomes
AF:
0.181
AC:
44832
AN:
247198
AF XY:
0.173
show subpopulations
Gnomad AFR exome
AF:
0.0433
Gnomad AMR exome
AF:
0.301
Gnomad ASJ exome
AF:
0.191
Gnomad EAS exome
AF:
0.214
Gnomad FIN exome
AF:
0.190
Gnomad NFE exome
AF:
0.187
Gnomad OTH exome
AF:
0.199
GnomAD4 exome
AF:
0.181
AC:
264190
AN:
1459688
Hom.:
25495
Cov.:
31
AF XY:
0.177
AC XY:
128717
AN XY:
726098
show subpopulations
African (AFR)
AF:
0.0428
AC:
1430
AN:
33430
American (AMR)
AF:
0.291
AC:
12945
AN:
44516
Ashkenazi Jewish (ASJ)
AF:
0.186
AC:
4864
AN:
26084
East Asian (EAS)
AF:
0.198
AC:
7828
AN:
39552
South Asian (SAS)
AF:
0.0671
AC:
5774
AN:
86080
European-Finnish (FIN)
AF:
0.190
AC:
10109
AN:
53342
Middle Eastern (MID)
AF:
0.184
AC:
1026
AN:
5564
European-Non Finnish (NFE)
AF:
0.188
AC:
209381
AN:
1110840
Other (OTH)
AF:
0.180
AC:
10833
AN:
60280
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.474
Heterozygous variant carriers
0
10145
20291
30436
40582
50727
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Exome Hom
Variant carriers
0
7272
14544
21816
29088
36360
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome
AF:
0.156
AC:
23676
AN:
152184
Hom.:
2232
Cov.:
32
AF XY:
0.155
AC XY:
11566
AN XY:
74396
show subpopulations
African (AFR)
AF:
0.0510
AC:
2117
AN:
41550
American (AMR)
AF:
0.257
AC:
3930
AN:
15268
Ashkenazi Jewish (ASJ)
AF:
0.196
AC:
681
AN:
3466
East Asian (EAS)
AF:
0.219
AC:
1132
AN:
5176
South Asian (SAS)
AF:
0.0750
AC:
362
AN:
4826
European-Finnish (FIN)
AF:
0.183
AC:
1941
AN:
10602
Middle Eastern (MID)
AF:
0.207
AC:
61
AN:
294
European-Non Finnish (NFE)
AF:
0.189
AC:
12846
AN:
67982
Other (OTH)
AF:
0.193
AC:
407
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
1006
2012
3017
4023
5029
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
250
500
750
1000
1250
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.174
Hom.:
8525
Bravo
AF:
0.158
Asia WGS
AF:
0.155
AC:
542
AN:
3478
EpiCase
AF:
0.180
EpiControl
AF:
0.188

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.66
CADD
Benign
5.7
DANN
Benign
0.84
PhyloP100
-1.3
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7
Mutation Taster
=100/0
polymorphism (auto)

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.050
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs561; hg19: chr19-8376431; COSMIC: COSV56846606; COSMIC: COSV56846606; API