2-163621341-C-T

Variant names:

• chr2-163621341-C-T
• rs7589522
• NM_018086.4:c.26-9535G>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_018086.4(FIGN):​c.26-9535G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.389 in 151,748 control chromosomes in the GnomAD database, including 13,211 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 0.39 (13211 hom., cov: 32)
• Consequence: FIGN NM_018086.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0830
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.29).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.593 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018086.4. 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
	FIGN	NM_018086.4	MANE Select	c.26-9535G>A		intron	N/A	NP_060556.2	Q5HY92
	FIGN	NM_001321825.2		c.-8-9535G>A		intron	N/A	NP_001308754.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FIGN	ENST00000333129.4	TSL:1 MANE Select	c.26-9535G>A		intron	N/A	ENSP00000333836.3	Q5HY92
	FIGN	ENST00000879555.1		c.26-9535G>A		intron	N/A	ENSP00000549614.1
	FIGN	ENST00000409634.5	TSL:5	c.26-27545G>A		intron	N/A	ENSP00000386768.1	B8ZZS6

Frequencies

GnomAD3 genomes AF: 0.389 AC: 58970 AN: 151630 Hom.: 13185 Cov.: 32

Gnomad AFR AF: 0.599

Gnomad AMI AF: 0.111

Gnomad AMR AF: 0.321

Gnomad ASJ AF: 0.374

Gnomad EAS AF: 0.573

Gnomad SAS AF: 0.375

Gnomad FIN AF: 0.376

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.271

Gnomad OTH AF: 0.370

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

GnomAD4 genome AF: 0.389 AC: 59053 AN: 151748 Hom.: 13211 Cov.: 32 AF XY: 0.393 AC XY: 29127 AN XY: 74136

African (AFR) AF: 0.599 AC: 24778 AN: 41380

American (AMR) AF: 0.321 AC: 4882 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.374 AC: 1296 AN: 3466

East Asian (EAS) AF: 0.572 AC: 2943 AN: 5144

South Asian (SAS) AF: 0.375 AC: 1805 AN: 4816

European-Finnish (FIN) AF: 0.376 AC: 3952 AN: 10522

Middle Eastern (MID) AF: 0.303 AC: 89 AN: 294

European-Non Finnish (NFE) AF: 0.271 AC: 18413 AN: 67882

Other (OTH) AF: 0.377 AC: 794 AN: 2104

Alfa AF: 0.314 Hom.: 12772

Bravo AF: 0.395

Asia WGS AF: 0.498 AC: 1730 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.29
CADD	Benign	15
DANN	Benign	0.80
PhyloP100		0.083
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: rs7589522; hg19: chr2-164477851;