chr2-152580056-C-T

Variant names:

• chr2-152580056-C-T
• rs11675841
• NM_052905.4:c.783-900C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_052905.4(FMNL2):​c.783-900C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.346 in 152,110 control chromosomes in the GnomAD database, including 10,024 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 0.35 (10024 hom., cov: 33)
• Consequence: FMNL2 NM_052905.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.47
• Publications: 8 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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.541 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.783-900C>T		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.783-900C>T		intron	N/A	ENSP00000288670.9
	FMNL2	ENST00000475377.3	TSL:5	c.783-900C>T		intron	N/A	ENSP00000418959.3
	FMNL2	ENST00000850952.1		c.783-900C>T		intron	N/A	ENSP00000521036.1

Frequencies

GnomAD3 genomes AF: 0.346 AC: 52646 AN: 151992 Hom.: 10036 Cov.: 33

Gnomad AFR AF: 0.188

Gnomad AMI AF: 0.554

Gnomad AMR AF: 0.313

Gnomad ASJ AF: 0.449

Gnomad EAS AF: 0.558

Gnomad SAS AF: 0.390

Gnomad FIN AF: 0.487

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.400

Gnomad OTH AF: 0.367

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

GnomAD4 genome AF: 0.346 AC: 52621 AN: 152110 Hom.: 10024 Cov.: 33 AF XY: 0.352 AC XY: 26184 AN XY: 74342

African (AFR) AF: 0.188 AC: 7809 AN: 41500

American (AMR) AF: 0.312 AC: 4772 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.449 AC: 1557 AN: 3468

East Asian (EAS) AF: 0.558 AC: 2887 AN: 5170

South Asian (SAS) AF: 0.389 AC: 1880 AN: 4832

European-Finnish (FIN) AF: 0.487 AC: 5145 AN: 10560

Middle Eastern (MID) AF: 0.497 AC: 146 AN: 294

European-Non Finnish (NFE) AF: 0.399 AC: 27158 AN: 67986

Other (OTH) AF: 0.361 AC: 762 AN: 2110

Alfa AF: 0.373 Hom.: 19568

Bravo AF: 0.328

Asia WGS AF: 0.393 AC: 1362 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.58
DANN	Benign	0.61
PhyloP100		-1.5
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: rs11675841; hg19: chr2-153436570;