chr2-163609899-T-C

Variant names:

• chr2-163609899-T-C
• rs1691196308
• NM_018086.4:c.1933A>G

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_018086.4(FIGN):​c.1933A>G​(p.Met645Val) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: FIGN NM_018086.4 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 3.67

Genes affected

FIGN (HGNC:13285): (fidgetin, microtubule severing factor) Predicted to enable microtubule-severing ATPase activity. Predicted to be involved in cytoplasmic microtubule organization. Predicted to act upstream of or within locomotory behavior. Predicted to be located in nuclear matrix. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.1566588).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FIGN	NM_018086.4	c.1933A>G	p.Met645Val	missense_variant	Exon 3 of 3	ENST00000333129.4	NP_060556.2
FIGN	NM_001321825.2	c.1900A>G	p.Met634Val	missense_variant	Exon 2 of 2		NP_001308754.1
FIGN	XM_047444863.1	c.2011A>G	p.Met671Val	missense_variant	Exon 3 of 3		XP_047300819.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FIGN	ENST00000333129.4	c.1933A>G	p.Met645Val	missense_variant	Exon 3 of 3	1	NM_018086.4	ENSP00000333836.3
FIGN	ENST00000409634.5	c.26-16103A>G		intron_variant	Intron 2 of 2	5		ENSP00000386768.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 37

GnomAD4 genome Cov.: 32

Bravo AF: 0.00000378

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Sep 14, 2021

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.1933A>G (p.M645V) alteration is located in exon 3 (coding exon 2) of the FIGN gene. This alteration results from a A to G substitution at nucleotide position 1933, causing the methionine (M) at amino acid position 645 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.062
BayesDel_addAF	Uncertain	0.041	T
BayesDel_noAF	Benign	-0.18
CADD	Benign	21
DANN	Benign	0.51
DEOGEN2	Benign	0.32	T
Eigen	Benign	-0.48
Eigen_PC	Benign	-0.18
FATHMM_MKL	Uncertain	0.91	D
LIST_S2	Uncertain	0.87	D
M_CAP	Benign	0.046	D
MetaRNN	Benign	0.16	T
MetaSVM	Uncertain	-0.26	T
MutationAssessor	Benign	-0.81	N
PrimateAI	Uncertain	0.66	T
PROVEAN	Benign	1.6	N
REVEL	Uncertain	0.30
Sift	Benign	1.0	T
Sift4G	Benign	0.39	T
Polyphen		0.012	B
Vest4		0.17
MutPred		0.56		Gain of methylation at K646 (P = 0.0229);
MVP		0.18
MPC		0.22
ClinPred		0.43	T
GERP RS		4.6
Varity_R		0.074
gMVP		0.42

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: rs1691196308; hg19: chr2-164466409;