chr2-163641436-C-G

Position:

• chr2-163641436-C-G

Variant summary

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

The NM_018086.4(FIGN):​c.26-29630G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.863 in 152,178 control chromosomes in the GnomAD database, including 56,793 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 0.86 (56793 hom., cov: 32)
• Consequence: FIGN NM_018086.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.372

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=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.888 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FIGN	NM_018086.4	c.26-29630G>C		intron_variant		ENST00000333129.4	NP_060556.2
FIGN	NM_001321825.2	c.-8-29630G>C		intron_variant			NP_001308754.1
FIGN	XM_047444863.1	c.-153-28852G>C		intron_variant			XP_047300819.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FIGN	ENST00000333129.4	c.26-29630G>C		intron_variant		1	NM_018086.4	ENSP00000333836.3
FIGN	ENST00000409634.5	c.26-47640G>C		intron_variant		5		ENSP00000386768.1
FIGN	ENST00000482917.1	n.148-29630G>C		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.863 AC: 131179 AN: 152060 Hom.: 56765 Cov.: 32

Gnomad AFR AF: 0.818

Gnomad AMI AF: 0.910

Gnomad AMR AF: 0.868

Gnomad ASJ AF: 0.882

Gnomad EAS AF: 0.776

Gnomad SAS AF: 0.840

Gnomad FIN AF: 0.868

Gnomad MID AF: 0.921

Gnomad NFE AF: 0.894

Gnomad OTH AF: 0.851

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

GnomAD4 genome AF: 0.863 AC: 131257 AN: 152178 Hom.: 56793 Cov.: 32 AF XY: 0.862 AC XY: 64088 AN XY: 74390

Gnomad4 AFR AF: 0.818

Gnomad4 AMR AF: 0.868

Gnomad4 ASJ AF: 0.882

Gnomad4 EAS AF: 0.777

Gnomad4 SAS AF: 0.840

Gnomad4 FIN AF: 0.868

Gnomad4 NFE AF: 0.894

Gnomad4 OTH AF: 0.845

Alfa AF: 0.861 Hom.: 2784

Bravo AF: 0.861

Asia WGS AF: 0.760 AC: 2641 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.3
DANN	Benign	0.55

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: rs2119289; hg19: chr2-164497946;