Variant rs7132908 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -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

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 made for transcript

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FAIM2	NM_012306.4 linkuse as main transcript	c.*1139C>T		3_prime_UTR_variant	12/12	ENST00000320634.8
FAIM2	XM_005268730.4 linkuse as main transcript	c.*1139C>T		3_prime_UTR_variant	11/11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FAIM2	ENST00000320634.8 linkuse as main transcript	c.*1139C>T		3_prime_UTR_variant	12/12	1	NM_012306.4	P1	Q9BWQ8-1

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

Gnomad4 AFR exome

AF:

0.250

Gnomad4 EAS exome

AF:

0.100

Gnomad4 SAS exome

AF:

0.667

Gnomad4 FIN exome

AF:

0.391

Gnomad4 NFE exome

AF:

0.377

Gnomad4 OTH exome

AF:

0.286

GnomAD4 genome

AF:

0.310

AC:

47126

AN:

152126

Hom.:

8209

Cov.:

AF XY:

0.309

AC XY:

22962

AN XY:

74370

show subpopulations

Gnomad4 AFR

AF:

0.155

Gnomad4 AMR

AF:

0.267

Gnomad4 ASJ

AF:

0.480

Gnomad4 EAS

AF:

0.229

Gnomad4 SAS

AF:

0.383

Gnomad4 FIN

AF:

0.377

Gnomad4 NFE

AF:

0.394

Gnomad4 OTH

AF:

0.310

Alfa

AF:

0.366

Hom.:

17701

Bravo

AF:

0.289

Asia WGS

AF:

0.259

AC:

903

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.18

CADD

Benign

DANN

Benign

0.84

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over