dbSNP rs811322: FAIM:c.-17+2083G>A (chr3-138611020-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_001033031.2(FAIM):c.-17+2083G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.6 in 1,611,770 control chromosomes in the GnomAD database, including 296,357 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 0.60 ( 28365 hom., cov: 32)

Exomes 𝑓: 0.60 ( 267992 hom. )

Consequence

FAIM
NM_001033031.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.499

Publications

28 publications found

Variant links:

Genes affected

FAIM (HGNC:18703): (Fas apoptotic inhibitory molecule) The protein encoded by this gene protects against death receptor-triggered apoptosis and regulates B-cell signaling and differentiation. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2011]

FAIM 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=-1.0).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.962 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FAIM	NM_001033031.2 link	c.-17+2083G>A		intron_variant	Intron 1 of 5	ENST00000360570.8	NP_001028203.1	Q9NVQ4-3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FAIM	ENST00000360570.8 link	c.-17+2083G>A		intron_variant	Intron 1 of 5	3	NM_001033031.2	ENSP00000353775.3		Q9NVQ4-3

Frequencies

GnomAD3 genomes

AF:

0.603

AC:

91614

AN:

151900

Hom.:

28327

Cov.:

show subpopulations

Gnomad AFR

AF:

0.556

Gnomad AMI

AF:

0.471

Gnomad AMR

AF:

0.676

Gnomad ASJ

AF:

0.503

Gnomad EAS

AF:

0.984

Gnomad SAS

AF:

0.738

Gnomad FIN

AF:

0.700

Gnomad MID

AF:

0.582

Gnomad NFE

AF:

0.569

Gnomad OTH

AF:

0.583

GnomAD2 exomes

AF:

0.657

AC:

165200

AN:

251334

AF XY:

0.653

show subpopulations

Gnomad AFR exome

AF:

0.566

Gnomad AMR exome

AF:

0.781

Gnomad ASJ exome

AF:

0.506

Gnomad EAS exome

AF:

0.990

Gnomad FIN exome

AF:

0.694

Gnomad NFE exome

AF:

0.567

Gnomad OTH exome

AF:

0.622

GnomAD4 exome

AF:

0.599

AC:

874658

AN:

1459754

Hom.:

267992

Cov.:

AF XY:

0.601

AC XY:

436860

AN XY:

726336

show subpopulations

African (AFR)

AF:

0.564

AC:

18852

AN:

33438

American (AMR)

AF:

0.768

AC:

34327

AN:

44698

Ashkenazi Jewish (ASJ)

AF:

0.503

AC:

13130

AN:

26104

East Asian (EAS)

AF:

0.984

AC:

39075

AN:

39694

South Asian (SAS)

AF:

0.725

AC:

62468

AN:

86206

European-Finnish (FIN)

AF:

0.693

AC:

37024

AN:

53400

Middle Eastern (MID)

AF:

0.561

AC:

3232

AN:

5762

European-Non Finnish (NFE)

AF:

0.567

AC:

629749

AN:

1110134

Other (OTH)

AF:

0.610

AC:

36801

AN:

60318

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.459

Heterozygous variant carriers

16587

33175

49762

66350

82937

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

17680

35360

53040

70720

88400

<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:

0.603

AC:

91699

AN:

152016

Hom.:

28365

Cov.:

AF XY:

0.615

AC XY:

45714

AN XY:

74304

show subpopulations

African (AFR)

AF:

0.557

AC:

23067

AN:

41444

American (AMR)

AF:

0.677

AC:

10341

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.503

AC:

1746

AN:

3468

East Asian (EAS)

AF:

0.985

AC:

5102

AN:

5182

South Asian (SAS)

AF:

0.737

AC:

3555

AN:

4822

European-Finnish (FIN)

AF:

0.700

AC:

7392

AN:

10562

Middle Eastern (MID)

AF:

0.575

AC:

169

AN:

294

European-Non Finnish (NFE)

AF:

0.569

AC:

38657

AN:

67944

Other (OTH)

AF:

0.588

AC:

1241

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1821

3641

5462

7282

9103

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

768

1536

2304

3072

3840

<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:

0.579

Hom.:

106513

Bravo

AF:

0.602

Asia WGS

AF:

0.839

AC:

2915

AN:

3478

EpiCase

AF:

0.568

EpiControl

AF:

0.555

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

7.7

(source)

DANN

Benign

0.45

PhyloP100

0.50

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