Genetic Variant AIFM2:c.*353C>T (chr10-70113825-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_032797.6(AIFM2):c.*353C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.226 in 202,254 control chromosomes in the GnomAD database, including 6,769 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 0.25 ( 5944 hom., cov: 32)

Exomes 𝑓: 0.16 ( 825 hom. )

Consequence

AIFM2
NM_032797.6 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.948

Publications

5 publications found

Variant links:

Genes affected

AIFM2 (HGNC:21411): (apoptosis inducing factor mitochondria associated 2) This gene encodes a flavoprotein oxidoreductase that binds single stranded DNA and is thought to contribute to apoptosis in the presence of bacterial and viral DNA. The expression of this gene is also found to be induced by tumor suppressor protein p53 in colon cancer cells. [provided by RefSeq, Nov 2010]

AIFM2 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=-0.91).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.424 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AIFM2	NM_032797.6 link	c.*353C>T		3_prime_UTR_variant	Exon 9 of 9	ENST00000307864.3	NP_116186.1	Q9BRQ8-1
AIFM2	NM_001198696.2 link	c.*353C>T		3_prime_UTR_variant	Exon 9 of 9		NP_001185625.1	Q9BRQ8-1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
AIFM2	ENST00000307864.3 link	c.*353C>T	3_prime_UTR_variant	Exon 9 of 9	1	NM_032797.6	ENSP00000312370.1	Q9BRQ8-1
AIFM2	ENST00000373248.5 link	c.*33+320C>T	intron_variant	Intron 8 of 8	1		ENSP00000362345.1	Q9BRQ8-1
AIFM2	ENST00000613322.4 link	c.*353C>T	3_prime_UTR_variant	Exon 9 of 9	5		ENSP00000478931.1	Q9BRQ8-1

Frequencies

GnomAD3 genomes

AF:

0.248

AC:

37644

AN:

151818

Hom.:

5937

Cov.:

show subpopulations

Gnomad AFR

AF:

0.429

Gnomad AMI

AF:

0.144

Gnomad AMR

AF:

0.245

Gnomad ASJ

AF:

0.222

Gnomad EAS

AF:

0.366

Gnomad SAS

AF:

0.299

Gnomad FIN

AF:

0.171

Gnomad MID

AF:

0.380

Gnomad NFE

AF:

0.140

Gnomad OTH

AF:

0.240

GnomAD4 exome

AF:

0.157

AC:

7921

AN:

50318

Hom.:

825

Cov.:

AF XY:

0.163

AC XY:

4241

AN XY:

26016

show subpopulations

African (AFR)

AF:

0.419

AC:

394

AN:

940

American (AMR)

AF:

0.228

AC:

379

AN:

1664

Ashkenazi Jewish (ASJ)

AF:

0.190

AC:

268

AN:

1414

East Asian (EAS)

AF:

0.313

AC:

411

AN:

1312

South Asian (SAS)

AF:

0.246

AC:

1428

AN:

5812

European-Finnish (FIN)

AF:

0.141

AC:

359

AN:

2544

Middle Eastern (MID)

AF:

0.227

AC:

AN:

220

European-Non Finnish (NFE)

AF:

0.124

AC:

4123

AN:

33290

Other (OTH)

AF:

0.163

AC:

509

AN:

3122

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.495

Heterozygous variant carriers

307

614

922

1229

1536

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

126

168

210

<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:

0.248

AC:

37688

AN:

151936

Hom.:

5944

Cov.:

AF XY:

0.252

AC XY:

18714

AN XY:

74264

show subpopulations

African (AFR)

AF:

0.429

AC:

17771

AN:

41398

American (AMR)

AF:

0.245

AC:

3743

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.222

AC:

771

AN:

3466

East Asian (EAS)

AF:

0.365

AC:

1877

AN:

5136

South Asian (SAS)

AF:

0.300

AC:

1444

AN:

4820

European-Finnish (FIN)

AF:

0.171

AC:

1801

AN:

10552

Middle Eastern (MID)

AF:

0.374

AC:

110

AN:

294

European-Non Finnish (NFE)

AF:

0.140

AC:

9535

AN:

67972

Other (OTH)

AF:

0.240

AC:

505

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1329

2657

3986

5314

6643

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

378

756

1134

1512

1890

<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:

0.180

Hom.:

1481

Bravo

AF:

0.261

Asia WGS

AF:

0.333

AC:

1159

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.27

(source)

DANN

Benign

0.39

PhyloP100

-0.95

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over