rs1027711

Variant names:

• chr12-49894249-A-G
• rs1027711
• NM_012306.4:c.434+2782T>C

Your query was ambiguous. Multiple possible variants found:

• chr12-49894249-A-G
• chr12-49894249-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_012306.4(FAIM2):​c.434+2782T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.11 in 152,232 control chromosomes in the GnomAD database, including 1,087 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 0.11 (1087 hom., cov: 32)
• Consequence: FAIM2 NM_012306.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.194
• Publications: 4 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.151 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_012306.4. 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
	FAIM2	NM_012306.4	MANE Select	c.434+2782T>C		intron	N/A	NP_036438.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAIM2	ENST00000320634.8	TSL:1 MANE Select	c.434+2782T>C		intron	N/A	ENSP00000321951.3
	FAIM2	ENST00000947305.1		c.452+2782T>C		intron	N/A	ENSP00000617364.1
	FAIM2	ENST00000947304.1		c.434+2782T>C		intron	N/A	ENSP00000617363.1

Frequencies

GnomAD3 genomes AF: 0.110 AC: 16760 AN: 152114 Hom.: 1083 Cov.: 32

Gnomad AFR AF: 0.0660

Gnomad AMI AF: 0.193

Gnomad AMR AF: 0.0808

Gnomad ASJ AF: 0.0795

Gnomad EAS AF: 0.0125

Gnomad SAS AF: 0.0519

Gnomad FIN AF: 0.123

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.154

Gnomad OTH AF: 0.117

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.110 AC: 16775 AN: 152232 Hom.: 1087 Cov.: 32 AF XY: 0.105 AC XY: 7817 AN XY: 74434

African (AFR) AF: 0.0660 AC: 2744 AN: 41550

American (AMR) AF: 0.0807 AC: 1234 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0795 AC: 276 AN: 3472

East Asian (EAS) AF: 0.0125 AC: 65 AN: 5182

South Asian (SAS) AF: 0.0511 AC: 247 AN: 4832

European-Finnish (FIN) AF: 0.123 AC: 1305 AN: 10600

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.154 AC: 10450 AN: 67984

Other (OTH) AF: 0.123 AC: 261 AN: 2116

Alfa AF: 0.139 Hom.: 3972

Bravo AF: 0.107

Asia WGS AF: 0.0760 AC: 263 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.3
DANN	Benign	0.60
PhyloP100		0.19
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: rs1027711; hg19: chr12-50288032;