2-163612676-G-T

Position:

• chr2-163612676-G-T

Variant summary

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

The ENST00000333129.4(FIGN):​c.26-870C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.598 in 914,732 control chromosomes in the GnomAD database, including 170,097 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 0.46 (18554 hom., cov: 26)
  • Exomes 𝑓: 0.62 (151543 hom.)
• Consequence: FIGN ENST00000333129.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.11

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 Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.622 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FIGN	NM_018086.4	c.26-870C>A		intron_variant		ENST00000333129.4	NP_060556.2
FIGN	NM_001321825.2	c.-8-870C>A		intron_variant			NP_001308754.1
FIGN	XM_047444863.1	c.-153-92C>A		intron_variant			XP_047300819.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FIGN	ENST00000333129.4	c.26-870C>A		intron_variant		1	NM_018086.4	ENSP00000333836	P1
FIGN	ENST00000409634.5	c.26-18880C>A		intron_variant		5		ENSP00000386768
FIGN	ENST00000482917.1	n.148-870C>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.464 AC: 66985 AN: 144410 Hom.: 18565 Cov.: 26

Gnomad AFR AF: 0.131

Gnomad AMI AF: 0.775

Gnomad AMR AF: 0.437

Gnomad ASJ AF: 0.501

Gnomad EAS AF: 0.443

Gnomad SAS AF: 0.528

Gnomad FIN AF: 0.583

Gnomad MID AF: 0.507

Gnomad NFE AF: 0.627

Gnomad OTH AF: 0.475

GnomAD4 exome AF: 0.623 AC: 479967 AN: 770220 Hom.: 151543 AF XY: 0.625 AC XY: 223712 AN XY: 357798

Gnomad4 AFR exome AF: 0.0874

Gnomad4 AMR exome AF: 0.411

Gnomad4 ASJ exome AF: 0.517

Gnomad4 EAS exome AF: 0.424

Gnomad4 SAS exome AF: 0.546

Gnomad4 FIN exome AF: 0.620

Gnomad4 NFE exome AF: 0.640

Gnomad4 OTH exome AF: 0.567

GnomAD4 genome AF: 0.463 AC: 66957 AN: 144512 Hom.: 18554 Cov.: 26 AF XY: 0.462 AC XY: 32410 AN XY: 70148

Gnomad4 AFR AF: 0.131

Gnomad4 AMR AF: 0.437

Gnomad4 ASJ AF: 0.501

Gnomad4 EAS AF: 0.444

Gnomad4 SAS AF: 0.527

Gnomad4 FIN AF: 0.583

Gnomad4 NFE AF: 0.627

Gnomad4 OTH AF: 0.469

Alfa AF: 0.581 Hom.: 51302

Bravo AF: 0.418

Asia WGS AF: 0.417 AC: 1449 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.8
DANN	Benign	0.67

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: rs12692701; hg19: chr2-164469186;