Genetic Variant AFG3L1P:n.1304A>C (chr16-90000528-A-C) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The ENST00000355531.7(AFG3L1P):n.1304A>C variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.692 in 157,502 control chromosomes in the GnomAD database, including 37,786 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 0.69 ( 36454 hom., cov: 32)

Exomes 𝑓: 0.70 ( 1332 hom. )

Consequence

AFG3L1P
ENST00000355531.7 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 6.88

Publications

80 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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new If you want to explore the variant's impact on the transcript ENST00000355531.7, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.44).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.741 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000355531.7. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AFG3L1P	NR_003228.1		n.1682A>C		non_coding_transcript_exon	Exon 13 of 13

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
AFG3L1P	ENST00000355531.7	TSL:1	n.1304A>C	non_coding_transcript_exon	Exon 7 of 7
AFG3L1P	ENST00000388970.8	TSL:1	n.1665A>C	non_coding_transcript_exon	Exon 13 of 13
AFG3L1P	ENST00000454997.1	TSL:2	n.1694A>C	non_coding_transcript_exon	Exon 3 of 3

Frequencies

GnomAD3 genomes

AF:

0.692

AC:

105151

AN:

151914

Hom.:

36429

Cov.:

show subpopulations

Gnomad AFR

AF:

0.682

Gnomad AMI

AF:

0.657

Gnomad AMR

AF:

0.752

Gnomad ASJ

AF:

0.674

Gnomad EAS

AF:

0.738

Gnomad SAS

AF:

0.752

Gnomad FIN

AF:

0.738

Gnomad MID

AF:

0.699

Gnomad NFE

AF:

0.671

Gnomad OTH

AF:

0.714

GnomAD4 exome

AF:

0.696

AC:

3807

AN:

5470

Hom.:

1332

Cov.:

AF XY:

0.691

AC XY:

2028

AN XY:

2934

show subpopulations

African (AFR)

AF:

0.734

AC:

AN:

American (AMR)

AF:

0.700

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.618

AC:

AN:

110

East Asian (EAS)

AF:

0.872

AC:

546

AN:

626

South Asian (SAS)

AF:

0.842

AC:

AN:

European-Finnish (FIN)

AF:

0.742

AC:

787

AN:

1060

Middle Eastern (MID)

AF:

0.667

AC:

AN:

European-Non Finnish (NFE)

AF:

0.648

AC:

2045

AN:

3156

Other (OTH)

AF:

0.669

AC:

202

AN:

302

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

106

158

211

264

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<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:

0.692

AC:

105220

AN:

152032

Hom.:

36454

Cov.:

AF XY:

0.699

AC XY:

51931

AN XY:

74302

show subpopulations

African (AFR)

AF:

0.682

AC:

28258

AN:

41460

American (AMR)

AF:

0.753

AC:

11508

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.674

AC:

2340

AN:

3472

East Asian (EAS)

AF:

0.737

AC:

3787

AN:

5140

South Asian (SAS)

AF:

0.753

AC:

3627

AN:

4818

European-Finnish (FIN)

AF:

0.738

AC:

7806

AN:

10574

Middle Eastern (MID)

AF:

0.701

AC:

206

AN:

294

European-Non Finnish (NFE)

AF:

0.671

AC:

45583

AN:

67966

Other (OTH)

AF:

0.714

AC:

1507

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.508

Heterozygous variant carriers

1714

3427

5141

6854

8568

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

818

1636

2454

3272

4090

<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:

0.677

Hom.:

166854

Bravo

AF:

0.687

Asia WGS

AF:

0.740

AC:

2574

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.44

CADD

Benign

8.1

(source)

DANN

Benign

0.62

PhyloP100

6.9

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over