chr2-131082624-C-T

Variant names:

• chr2-131082624-C-T
• NM_001009993.4:c.23G>A

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_001009993.4(FAM168B):​c.23G>A​(p.Gly8Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: FAM168B NM_001009993.4 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 3.55
• Publications: 0 publications found

Genes affected

FAM168B (HGNC:27016): (family with sequence similarity 168 member B) Located in extracellular exosome. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001009993.4. 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
	FAM168B	NM_001009993.4	MANE Select	c.23G>A	p.Gly8Glu	missense	Exon 2 of 7	NP_001009993.2	A1KXE4-1
	FAM168B	NM_001321743.1		c.23G>A	p.Gly8Glu	missense	Exon 4 of 9	NP_001308672.1	A1KXE4-1
	FAM168B	NM_001321744.1		c.23G>A	p.Gly8Glu	missense	Exon 3 of 8	NP_001308673.1	A1KXE4-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM168B	ENST00000389915.4	TSL:3 MANE Select	c.23G>A	p.Gly8Glu	missense	Exon 2 of 7	ENSP00000374565.3	A1KXE4-1
	FAM168B	ENST00000409185.5	TSL:1	c.23G>A	p.Gly8Glu	missense	Exon 2 of 7	ENSP00000387051.1	A1KXE4-1
	FAM168B	ENST00000894388.1		c.23G>A	p.Gly8Glu	missense	Exon 3 of 8	ENSP00000564447.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 28

GnomAD4 genome Cov.: 32

ClinVar

ClinVar submissions

Significance: Uncertain significance

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	1	-	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.33
BayesDel_addAF	Pathogenic	0.36	D
BayesDel_noAF	Pathogenic	0.28
CADD	Benign	23
DANN	Uncertain	0.99
DEOGEN2	Benign	0.054	T
Eigen	Uncertain	0.22
Eigen_PC	Uncertain	0.37
FATHMM_MKL	Uncertain	0.85	D
LIST_S2	Uncertain	0.89	D
M_CAP	Benign	0.0056	T
MetaRNN	Uncertain	0.44	T
MetaSVM	Benign	-0.89	T
MutationAssessor	Benign	0.34	N
PhyloP100		3.6
PrimateAI	Uncertain	0.78	T
PROVEAN	Benign	-2.4	N
REVEL	Uncertain	0.33
Sift	Benign	0.084	T
Sift4G	Benign	0.093	T
Polyphen		0.63	P
Vest4		0.77
MutPred		0.17		Gain of solvent accessibility (P = 0.0456)
MVP		0.13
MPC		0.75
ClinPred		0.67	D
GERP RS		5.7
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Varity_R		0.43
gMVP		0.75
Mutation Taster		=56/44	polymorphism

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

hg19: chr2-131840197;