rs7132908

Variant names:

• chr12-49869365-G-A
• rs7132908
• NM_012306.4:c.*1139C>T

Your query was ambiguous. Multiple possible variants found:

• chr12-49869365-G-A
• chr12-49869365-G-C

Variant summary

Our verdict is Benign. The variant received -9 ACMG points: 0P and 9B. BP4 BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.29
• Publications: 74 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
FAIM2	NM_012306.4	c.*1139C>T		3_prime_UTR_variant	Exon 12 of 12	ENST00000320634.8	NP_036438.2
FAIM2	XM_005268730.4	c.*1139C>T		3_prime_UTR_variant	Exon 11 of 11		XP_005268787.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FAIM2	ENST00000320634.8	c.*1139C>T		3_prime_UTR_variant	Exon 12 of 12	1	NM_012306.4	ENSP00000321951.3

Frequencies

GnomAD3 genomes AF: 0.310 AC: 47136 AN: 152008 Hom.: 8210 Cov.: 32

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.: 48 Cov.: 0 AF XY: 0.352 AC XY: 157 AN XY: 446

African (AFR) AF: 0.250 AC: 1 AN: 4

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.100 AC: 1 AN: 10

South Asian (SAS) AF: 0.667 AC: 4 AN: 6

European-Finnish (FIN) AF: 0.391 AC: 165 AN: 422

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4

European-Non Finnish (NFE) AF: 0.377 AC: 80 AN: 212

Other (OTH) AF: 0.286 AC: 4 AN: 14

GnomAD4 genome AF: 0.310 AC: 47126 AN: 152126 Hom.: 8209 Cov.: 32 AF XY: 0.309 AC XY: 22962 AN XY: 74370

African (AFR) AF: 0.155 AC: 6445 AN: 41522

American (AMR) AF: 0.267 AC: 4085 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.480 AC: 1666 AN: 3470

East Asian (EAS) AF: 0.229 AC: 1186 AN: 5170

South Asian (SAS) AF: 0.383 AC: 1847 AN: 4820

European-Finnish (FIN) AF: 0.377 AC: 3997 AN: 10590

Middle Eastern (MID) AF: 0.412 AC: 121 AN: 294

European-Non Finnish (NFE) AF: 0.394 AC: 26741 AN: 67950

Other (OTH) AF: 0.310 AC: 655 AN: 2110

Alfa AF: 0.359 Hom.: 37617

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	16
DANN	Benign	0.84
PhyloP100		1.3
Mutation Taster		=100/0	polymorphism (auto)

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: rs7132908; hg19: chr12-50263148; COSMIC: COSV57739186; COSMIC: COSV57739186;