Variant rs706795 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The NM_012306.4(FAIM2):c.-95A>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.575 in 1,341,232 control chromosomes in the GnomAD database, including 227,484 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 0.49 ( 20127 hom., cov: 33)

Exomes 𝑓: 0.59 ( 207357 hom. )

Consequence

FAIM2
NM_012306.4 5_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.32

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:

LINC02395 (HGNC:53322): (long intergenic non-protein coding RNA 2395)

LINC02395 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.35).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.713 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.-95A>G		5_prime_UTR_variant	1/12	ENST00000320634.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FAIM2	ENST00000320634.8 linkuse as main transcript	c.-95A>G		5_prime_UTR_variant	1/12	1	NM_012306.4	P1	Q9BWQ8-1
LINC02395	ENST00000657051.1 linkuse as main transcript	n.431+1246T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.489

AC:

74246

AN:

151934

Hom.:

20134

Cov.:

show subpopulations

Gnomad AFR

AF:

0.249

Gnomad AMI

AF:

0.542

Gnomad AMR

AF:

0.505

Gnomad ASJ

AF:

0.739

Gnomad EAS

AF:

0.340

Gnomad SAS

AF:

0.733

Gnomad FIN

AF:

0.602

Gnomad MID

AF:

0.715

Gnomad NFE

AF:

0.591

Gnomad OTH

AF:

0.540

GnomAD4 exome

AF:

0.586

AC:

696871

AN:

1189182

Hom.:

207357

Cov.:

AF XY:

0.591

AC XY:

345715

AN XY:

584918

show subpopulations

Gnomad4 AFR exome

AF:

0.238

Gnomad4 AMR exome

AF:

0.498

Gnomad4 ASJ exome

AF:

0.721

Gnomad4 EAS exome

AF:

0.361

Gnomad4 SAS exome

AF:

0.741

Gnomad4 FIN exome

AF:

0.596

Gnomad4 NFE exome

AF:

0.592

Gnomad4 OTH exome

AF:

0.576

GnomAD4 genome

AF:

0.488

AC:

74239

AN:

152050

Hom.:

20127

Cov.:

AF XY:

0.494

AC XY:

36750

AN XY:

74330

show subpopulations

Gnomad4 AFR

AF:

0.249

Gnomad4 AMR

AF:

0.505

Gnomad4 ASJ

AF:

0.739

Gnomad4 EAS

AF:

0.340

Gnomad4 SAS

AF:

0.733

Gnomad4 FIN

AF:

0.602

Gnomad4 NFE

AF:

0.591

Gnomad4 OTH

AF:

0.537

Alfa

AF:

0.574

Hom.:

43368

Bravo

AF:

0.465

Asia WGS

AF:

0.553

AC:

1919

AN:

3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.35

CADD

Benign

DANN

Benign

0.90

Splicing

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