2-163634019-A-T

Position:

• chr2-163634019-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_018086.4(FIGN):​c.26-22213T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.87 in 151,858 control chromosomes in the GnomAD database, including 57,538 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 0.87 (57538 hom., cov: 30)
• Consequence: FIGN NM_018086.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.407

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]

FIGN (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.889 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FIGN	NM_018086.4	c.26-22213T>A		intron_variant		ENST00000333129.4	NP_060556.2
FIGN	NM_001321825.2	c.-8-22213T>A		intron_variant			NP_001308754.1
FIGN	XM_047444863.1	c.-153-21435T>A		intron_variant			XP_047300819.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FIGN	ENST00000333129.4	c.26-22213T>A		intron_variant		1	NM_018086.4	ENSP00000333836.3
FIGN	ENST00000409634.5	c.26-40223T>A		intron_variant		5		ENSP00000386768.1
FIGN	ENST00000482917.1	n.148-22213T>A		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.870 AC: 131984 AN: 151740 Hom.: 57502 Cov.: 30

Gnomad AFR AF: 0.840

Gnomad AMI AF: 0.910

Gnomad AMR AF: 0.874

Gnomad ASJ AF: 0.882

Gnomad EAS AF: 0.778

Gnomad SAS AF: 0.841

Gnomad FIN AF: 0.870

Gnomad MID AF: 0.924

Gnomad NFE AF: 0.895

Gnomad OTH AF: 0.854

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

GnomAD4 genome AF: 0.870 AC: 132074 AN: 151858 Hom.: 57538 Cov.: 30 AF XY: 0.869 AC XY: 64451 AN XY: 74198

Gnomad4 AFR AF: 0.840

Gnomad4 AMR AF: 0.874

Gnomad4 ASJ AF: 0.882

Gnomad4 EAS AF: 0.779

Gnomad4 SAS AF: 0.841

Gnomad4 FIN AF: 0.870

Gnomad4 NFE AF: 0.895

Gnomad4 OTH AF: 0.848

Alfa AF: 0.882 Hom.: 6907

Bravo AF: 0.868

Asia WGS AF: 0.763 AC: 2652 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	4.8
DANN	Benign	0.33

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: rs982393; hg19: chr2-164490529;