Genetic Variant NDUFA6-DT:n.563T>C (chr22-42135691-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000621190.1(NDUFA6-DT):n.563T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. 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 0.28 ( 2189 hom., cov: 6)

Failed GnomAD Quality Control

Consequence

NDUFA6-DT
ENST00000621190.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.175

Publications

5 publications found

Variant links:

Genes affected

NDUFA6-DT (HGNC:45273): (NDUFA6 divergent transcript)

NDUFA6-DT links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.313 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NDUFA6-DT	ENST00000621190.1 link	n.563T>C		non_coding_transcript_exon_variant	Exon 5 of 8	5
NDUFA6-DT	ENST00000439129.5 link	n.1719-508T>C		intron_variant	Intron 5 of 6	5

Frequencies

GnomAD3 genomes

AF:

0.280

AC:

12640

AN:

45134

Hom.:

2180

Cov.:

show subpopulations

Gnomad AFR

AF:

0.293

Gnomad AMI

AF:

0.149

Gnomad AMR

AF:

0.294

Gnomad ASJ

AF:

0.355

Gnomad EAS

AF:

0.108

Gnomad SAS

AF:

0.341

Gnomad FIN

AF:

0.338

Gnomad MID

AF:

0.495

Gnomad NFE

AF:

0.280

Gnomad OTH

AF:

0.306

GnomAD4 exome

Data not reliable, filtered out with message: AC0;AS_VQSR

AC:

AN:

Hom.:

Cov.:

AC XY:

AN XY:

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AC:

AN:

Other (OTH)

AC:

AN:

GnomAD4 genome

AF:

0.280

AC:

12658

AN:

45156

Hom.:

2189

Cov.:

AF XY:

0.282

AC XY:

5524

AN XY:

19606

show subpopulations

African (AFR)

AF:

0.295

AC:

2965

AN:

10044

American (AMR)

AF:

0.295

AC:

1186

AN:

4022

Ashkenazi Jewish (ASJ)

AF:

0.355

AC:

447

AN:

1260

East Asian (EAS)

AF:

0.106

AC:

307

AN:

2898

South Asian (SAS)

AF:

0.340

AC:

432

AN:

1272

European-Finnish (FIN)

AF:

0.338

AC:

840

AN:

2486

Middle Eastern (MID)

AF:

0.488

AC:

AN:

170

European-Non Finnish (NFE)

AF:

0.280

AC:

6157

AN:

22024

Other (OTH)

AF:

0.303

AC:

187

AN:

618

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

368

736

1105

1473

1841

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

192

288

384

480

<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:

0.338

Hom.:

1331

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

7.7

(source)

PhyloP100

-0.17

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over