Genetic Variant AFG3L1P:n.170-19C>T (chr16-89977620-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000388970.8(AFG3L1P):n.170-19C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.402 in 152,330 control chromosomes in the GnomAD database, including 13,732 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 0.40 ( 13691 hom., cov: 32)

Exomes 𝑓: 0.48 ( 41 hom. )

Consequence

AFG3L1P
ENST00000388970.8 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.484

Publications

27 publications found

Variant links:

Genes affected

AFG3L1P (HGNC:):

AFG3L1P links:

AFG3L1P (HGNC:314): (AFG3 like matrix AAA peptidase subunit 1, pseudogene) Predicted to be involved in protein processing. Predicted to act upstream of or within cristae formation; mitochondrial fusion; and mitochondrial protein processing. Predicted to be located in mitochondrial inner membrane. Predicted to be part of m-AAA complex. [provided by Alliance of Genome Resources, Apr 2022]

AFG3L1P links:

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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=-0.85).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.559 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
AFG3L1P	NR_003226.1 link	n.202C>T	non_coding_transcript_exon_variant	Exon 2 of 11
AFG3L1P	NR_003227.1 link	n.187-58C>T	intron_variant	Intron 1 of 9
AFG3L1P	NR_003228.1 link	n.187-19C>T	intron_variant	Intron 1 of 12

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
AFG3L1P	ENST00000388970.8 link	n.170-19C>T	intron_variant	Intron 1 of 12	1
AFG3L1P	ENST00000421164.5 link	n.119-19C>T	intron_variant	Intron 1 of 5	1
AFG3L1P	ENST00000421780.6 link	n.178-19C>T	intron_variant	Intron 1 of 4	1

Frequencies

GnomAD3 genomes

AF:

0.402

AC:

60980

AN:

151832

Hom.:

13681

Cov.:

show subpopulations

Gnomad AFR

AF:

0.206

Gnomad AMI

AF:

0.606

Gnomad AMR

AF:

0.414

Gnomad ASJ

AF:

0.568

Gnomad EAS

AF:

0.188

Gnomad SAS

AF:

0.576

Gnomad FIN

AF:

0.423

Gnomad MID

AF:

0.601

Gnomad NFE

AF:

0.504

Gnomad OTH

AF:

0.468

GnomAD4 exome

AF:

0.481

AC:

182

AN:

378

Hom.:

Cov.:

AF XY:

0.496

AC XY:

111

AN XY:

224

show subpopulations

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)

AF:

0.476

AC:

177

AN:

372

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

1.00

AC:

AN:

Other (OTH)

AF:

0.750

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.401

AC:

61007

AN:

151952

Hom.:

13691

Cov.:

AF XY:

0.402

AC XY:

29812

AN XY:

74232

show subpopulations

African (AFR)

AF:

0.207

AC:

8563

AN:

41466

American (AMR)

AF:

0.413

AC:

6310

AN:

15260

Ashkenazi Jewish (ASJ)

AF:

0.568

AC:

1970

AN:

3470

East Asian (EAS)

AF:

0.189

AC:

975

AN:

5172

South Asian (SAS)

AF:

0.577

AC:

2777

AN:

4814

European-Finnish (FIN)

AF:

0.423

AC:

4446

AN:

10508

Middle Eastern (MID)

AF:

0.599

AC:

176

AN:

294

European-Non Finnish (NFE)

AF:

0.504

AC:

34254

AN:

67948

Other (OTH)

AF:

0.467

AC:

986

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1742

3484

5225

6967

8709

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

580

1160

1740

2320

2900

<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:

0.463

Hom.:

15054

Bravo

AF:

0.384

Asia WGS

AF:

0.391

AC:

1358

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

0.95

(source)

DANN

Benign

0.31

PhyloP100

-0.48

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