rs811322

chr3-138611020-G-Achr3-138611020-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.499

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]

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
FAIM	NM_001033031.2	c.-17+2083G>A		intron_variant		ENST00000360570.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FAIM	ENST00000360570.8	c.-17+2083G>A		intron_variant		3	NM_001033031.2

Frequencies

GnomAD3 genomes AF: 0.603 AC: 91614 AN: 151900 Hom.: 28327 Cov.: 32

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

GnomAD3 exomes AF: 0.657 AC: 165200 AN: 251334 Hom.: 56540 AF XY: 0.653 AC XY: 88640 AN XY: 135830

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 SAS exome AF: 0.730

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.: 38 AF XY: 0.601 AC XY: 436860 AN XY: 726336

Gnomad4 AFR exome AF: 0.564

Gnomad4 AMR exome AF: 0.768

Gnomad4 ASJ exome AF: 0.503

Gnomad4 EAS exome AF: 0.984

Gnomad4 SAS exome AF: 0.725

Gnomad4 FIN exome AF: 0.693

Gnomad4 NFE exome AF: 0.567

Gnomad4 OTH exome AF: 0.610

GnomAD4 genome AF: 0.603 AC: 91699 AN: 152016 Hom.: 28365 Cov.: 32 AF XY: 0.615 AC XY: 45714 AN XY: 74304

Gnomad4 AFR AF: 0.557

Gnomad4 AMR AF: 0.677

Gnomad4 ASJ AF: 0.503

Gnomad4 EAS AF: 0.985

Gnomad4 SAS AF: 0.737

Gnomad4 FIN AF: 0.700

Gnomad4 NFE AF: 0.569

Gnomad4 OTH AF: 0.588

Alfa AF: 0.571 Hom.: 47206

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
Dann	Benign	0.45

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

Other links and lift over

dbSNP: rs811322; hg19: chr3-138329862; COSMIC: COSV58158463;