3-138611020-G-T

Variant names:

• chr3-138611020-G-T
• rs811322
• NM_001033031.2:c.-17+2083G>T

Variant summary

Our verdict is Likely benign. The variant received -3 ACMG points: 2P and 5B. PM2 BP4_Strong BP7

The NM_001033030.2(FAIM):​c.63G>T​(p.Pro21Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• Consequence: FAIM NM_001033030.2 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.499
• Publications: 28 publications found

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

Our verdict: Likely_benign. The variant received -3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BP7: Synonymous conserved (PhyloP=0.499 with no splicing effect.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001033030.2. 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
	FAIM	NM_001033031.2	MANE Select	c.-17+2083G>T		intron	N/A	NP_001028203.1	Q9NVQ4-3
	FAIM	NM_001033030.2		c.63G>T	p.Pro21Pro	synonymous	Exon 2 of 6	NP_001028202.1	Q9NVQ4-2
	FAIM	NM_001033032.2		c.-23+2083G>T		intron	N/A	NP_001028204.1	Q9NVQ4-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAIM	ENST00000360570.8	TSL:3 MANE Select	c.-17+2083G>T		intron	N/A	ENSP00000353775.3	Q9NVQ4-3
	FAIM	ENST00000393035.6	TSL:1	c.-23+2083G>T		intron	N/A	ENSP00000376755.2	Q9NVQ4-1
	FAIM	ENST00000869303.1		c.-34G>T		5_prime_UTR_premature_start_codon_gain	Exon 2 of 7	ENSP00000539362.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 38

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 106513

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.8
DANN	Benign	0.46
PhyloP100		0.50

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

Other links and lift over

dbSNP: rs811322; hg19: chr3-138329862;