rs11675841

chr2-152580056-C-T

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FMNL2	NM_052905.4	c.783-900C>T		intron_variant		ENST00000288670.14

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FMNL2	ENST00000288670.14	c.783-900C>T		intron_variant		1	NM_052905.4	P1
FMNL2	ENST00000475377.3	c.783-900C>T		intron_variant		5
FMNL2	ENST00000492942.1	n.345-900C>T		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.188

Gnomad4 AMR AF: 0.312

Gnomad4 ASJ AF: 0.449

Gnomad4 EAS AF: 0.558

Gnomad4 SAS AF: 0.389

Gnomad4 FIN AF: 0.487

Gnomad4 NFE AF: 0.399

Gnomad4 OTH AF: 0.361

Alfa AF: 0.368 Hom.: 3994

Bravo AF: 0.328

Asia WGS AF: 0.393 AC: 1362 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.58
Dann	Benign	0.61

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: rs11675841; hg19: chr2-153436570;