chr12-51821010-C-T

Variant names:

• chr12-51821010-C-T
• rs1939165408
• NM_001384995.1:c.1404G>A

Variant summary

Our verdict is Likely benign. The variant received -1 ACMG points: 2P and 3B. PM2 BP4_Moderate BP7

The NM_001384995.1(FIGNL2):​c.1404G>A​(p.Glu468Glu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000971 in 1,030,388 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 32)
  • Exomes 𝑓: 9.7e-7 (0 hom.)
• Consequence: FIGNL2 NM_001384995.1 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.181
• Publications: 0 publications found

Genes affected

FIGNL2 (HGNC:13287): (fidgetin like 2) Predicted to enable microtubule-severing ATPase activity. Predicted to be involved in cytoplasmic microtubule organization. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000260473 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.36).
• BP7: Synonymous conserved (PhyloP=0.181 with no splicing effect.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001384995.1. 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
	FIGNL2	NM_001384995.1	MANE Select	c.1404G>A	p.Glu468Glu	synonymous	Exon 2 of 2	NP_001371924.1	A6NMB9
	FIGNL2	NM_001013690.5		c.1404G>A	p.Glu468Glu	synonymous	Exon 2 of 2	NP_001013712.4	A6NMB9
	FIGNL2	NM_001384996.1		c.1404G>A	p.Glu468Glu	synonymous	Exon 3 of 3	NP_001371925.1	A6NMB9

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FIGNL2	ENST00000618634.3	TSL:5 MANE Select	c.1404G>A	p.Glu468Glu	synonymous	Exon 2 of 2	ENSP00000491257.1	A6NMB9
	FIGNL2	ENST00000938505.1		c.1404G>A	p.Glu468Glu	synonymous	Exon 2 of 2	ENSP00000608564.1
	FIGNL2	ENST00000948593.1		c.1404G>A	p.Glu468Glu	synonymous	Exon 2 of 2	ENSP00000618652.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 9.71e-7 AC: 1 AN: 1030388 Hom.: 0 Cov.: 29 AF XY: 0.00000205 AC XY: 1 AN XY: 487230

African (AFR) AF: 0.00 AC: 0 AN: 20840

American (AMR) AF: 0.00 AC: 0 AN: 6644

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 11724

East Asian (EAS) AF: 0.00 AC: 0 AN: 21074

South Asian (SAS) AF: 0.00 AC: 0 AN: 19182

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 19132

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2634

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 889538

Other (OTH) AF: 0.0000252 AC: 1 AN: 39620

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.36
CADD	Benign	9.8
DANN	Benign	0.97
PhyloP100		0.18

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1939165408; hg19: chr12-52214794;