chr2-152639459-A-G

Variant names:

• chr2-152639459-A-G
• rs3811568
• NM_052905.4:c.2947-499A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

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]

ENSG00000286207 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_052905.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FMNL2	NM_052905.4	MANE Select	c.2947-499A>G		intron	N/A	NP_443137.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FMNL2	ENST00000288670.14	TSL:1 MANE Select	c.2947-499A>G		intron	N/A	ENSP00000288670.9
	ENSG00000286207	ENST00000650944.2		n.1817T>C		non_coding_transcript_exon	Exon 1 of 2
	FMNL2	ENST00000475377.3	TSL:5	c.2968-499A>G		intron	N/A	ENSP00000418959.3

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

African (AFR) AF: 0.0395 AC: 1642 AN: 41564

American (AMR) AF: 0.229 AC: 3496 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.215 AC: 745 AN: 3468

East Asian (EAS) AF: 0.0135 AC: 70 AN: 5170

South Asian (SAS) AF: 0.195 AC: 941 AN: 4826

European-Finnish (FIN) AF: 0.104 AC: 1107 AN: 10612

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.155 AC: 10543 AN: 67988

Other (OTH) AF: 0.148 AC: 312 AN: 2110

Alfa AF: 0.145 Hom.: 307

Bravo AF: 0.131

Asia WGS AF: 0.146 AC: 508 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.61
DANN	Benign	0.50
PhyloP100		-0.89
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: rs3811568; hg19: chr2-153495973;