Genetic Variant FAIM2:c.*1139C>T (chr12-49869365-G-A) – ACMG Classification: Benign (-9 pts)

Variant summary

Our verdict is Benign. The variant received -9 ACMG points: 0P and 9B. BP4BA1

The NM_012306.4(FAIM2):c.*1139C>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 0.31 in 152,798 control chromosomes in the GnomAD database, including 8,257 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 0.31 ( 8209 hom., cov: 32)

Exomes 𝑓: 0.38 ( 48 hom. )

Consequence

FAIM2
NM_012306.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.29

Publications

74 publications found

Variant links:

Genes affected

FAIM2 (HGNC:17067): (Fas apoptotic inhibitory molecule 2) Involved in regulation of neuron apoptotic process. Acts upstream of or within negative regulation of extrinsic apoptotic signaling pathway via death domain receptors. Located in membrane raft. [provided by Alliance of Genome Resources, Apr 2022]

FAIM2 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -9 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.18).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.39 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_012306.4. 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
	FAIM2	NM_012306.4	MANE Select	c.*1139C>T		3_prime_UTR	Exon 12 of 12	NP_036438.2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
FAIM2	ENST00000320634.8	TSL:1 MANE Select	c.*1139C>T	3_prime_UTR	Exon 12 of 12	ENSP00000321951.3
FAIM2	ENST00000947305.1		c.*1139C>T	3_prime_UTR	Exon 12 of 12	ENSP00000617364.1
FAIM2	ENST00000947304.1		c.*1139C>T	3_prime_UTR	Exon 12 of 12	ENSP00000617363.1

Frequencies

GnomAD3 genomes

AF:

0.310

AC:

47136

AN:

152008

Hom.:

8210

Cov.:

show subpopulations

Gnomad AFR

AF:

0.156

Gnomad AMI

AF:

0.420

Gnomad AMR

AF:

0.268

Gnomad ASJ

AF:

0.480

Gnomad EAS

AF:

0.229

Gnomad SAS

AF:

0.383

Gnomad FIN

AF:

0.377

Gnomad MID

AF:

0.411

Gnomad NFE

AF:

0.394

Gnomad OTH

AF:

0.314

GnomAD4 exome

AF:

0.379

AC:

255

AN:

672

Hom.:

Cov.:

AF XY:

0.352

AC XY:

157

AN XY:

446

show subpopulations

African (AFR)

AF:

0.250

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

0.100

AC:

AN:

South Asian (SAS)

AF:

0.667

AC:

AN:

European-Finnish (FIN)

AF:

0.391

AC:

165

AN:

422

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.377

AC:

AN:

212

Other (OTH)

AF:

0.286

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.310

AC:

47126

AN:

152126

Hom.:

8209

Cov.:

AF XY:

0.309

AC XY:

22962

AN XY:

74370

show subpopulations

African (AFR)

AF:

0.155

AC:

6445

AN:

41522

American (AMR)

AF:

0.267

AC:

4085

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.480

AC:

1666

AN:

3470

East Asian (EAS)

AF:

0.229

AC:

1186

AN:

5170

South Asian (SAS)

AF:

0.383

AC:

1847

AN:

4820

European-Finnish (FIN)

AF:

0.377

AC:

3997

AN:

10590

Middle Eastern (MID)

AF:

0.412

AC:

121

AN:

294

European-Non Finnish (NFE)

AF:

0.394

AC:

26741

AN:

67950

Other (OTH)

AF:

0.310

AC:

655

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1589

3178

4767

6356

7945

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

482

964

1446

1928

2410

<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:

0.359

Hom.:

37617

Bravo

AF:

0.289

Asia WGS

AF:

0.259

AC:

903

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.18

CADD

Benign

(source)

DANN

Benign

0.84

PhyloP100

1.3

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over