rs3811568

Positions:

• chr2-152639459-A-G

Variant summary

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

The NM_052905.4(FMNL2):​c.2947-499A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.126 in 152,232 control chromosomes in the GnomAD database, including 1,528 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 0.13 (1528 hom., cov: 32)
• Consequence: FMNL2 NM_052905.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.893

Genes affected

FMNL2 (HGNC:18267): (formin like 2) This gene encodes a formin-related protein. Formin-related proteins have been implicated in morphogenesis, cytokinesis, and cell polarity. Alternatively spliced transcript variants encoding different isoforms have been described but their full-length nature has yet to be determined. [provided by RefSeq, Jul 2008]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.222 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FMNL2	NM_052905.4	c.2947-499A>G		intron_variant		ENST00000288670.14

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FMNL2	ENST00000288670.14	c.2947-499A>G		intron_variant		1	NM_052905.4	P1
	ENST00000650944.1	n.1817T>C		non_coding_transcript_exon_variant	1/2
FMNL2	ENST00000475377.3	c.2968-499A>G		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.126 AC: 19178 AN: 152114 Hom.: 1529 Cov.: 32

Gnomad AFR AF: 0.0395

Gnomad AMI AF: 0.285

Gnomad AMR AF: 0.229

Gnomad ASJ AF: 0.215

Gnomad EAS AF: 0.0135

Gnomad SAS AF: 0.195

Gnomad FIN AF: 0.104

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.155

Gnomad OTH AF: 0.147

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

GnomAD4 genome AF: 0.126 AC: 19185 AN: 152232 Hom.: 1528 Cov.: 32 AF XY: 0.126 AC XY: 9394 AN XY: 74422

Gnomad4 AFR AF: 0.0395

Gnomad4 AMR AF: 0.229

Gnomad4 ASJ AF: 0.215

Gnomad4 EAS AF: 0.0135

Gnomad4 SAS AF: 0.195

Gnomad4 FIN AF: 0.104

Gnomad4 NFE AF: 0.155

Gnomad4 OTH AF: 0.148

Alfa AF: 0.148 Hom.: 306

Bravo AF: 0.131

Asia WGS AF: 0.146 AC: 508 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.61
DANN	Benign	0.50

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: rs3811568; hg19: chr2-153495973;