2-152582077-G-C

Position:

• chr2-152582077-G-C

Variant summary

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

The NM_052905.4(FMNL2):​c.876+1028G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0419 in 152,204 control chromosomes in the GnomAD database, including 231 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 0.042 (231 hom., cov: 32)
• Consequence: FMNL2 NM_052905.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0430

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]

FMNL2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0576 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FMNL2	NM_052905.4	c.876+1028G>C		intron_variant		ENST00000288670.14	NP_443137.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FMNL2	ENST00000288670.14	c.876+1028G>C		intron_variant		1	NM_052905.4	ENSP00000288670.9
FMNL2	ENST00000475377.3	c.876+1028G>C		intron_variant		5		ENSP00000418959.3
FMNL2	ENST00000492942.1	n.438+1028G>C		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.0420 AC: 6381 AN: 152086 Hom.: 231 Cov.: 32

Gnomad AFR AF: 0.00905

Gnomad AMI AF: 0.0824

Gnomad AMR AF: 0.0273

Gnomad ASJ AF: 0.0386

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0126

Gnomad FIN AF: 0.116

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0591

Gnomad OTH AF: 0.0321

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

GnomAD4 genome AF: 0.0419 AC: 6380 AN: 152204 Hom.: 231 Cov.: 32 AF XY: 0.0428 AC XY: 3183 AN XY: 74424

Gnomad4 AFR AF: 0.00903

Gnomad4 AMR AF: 0.0273

Gnomad4 ASJ AF: 0.0386

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0127

Gnomad4 FIN AF: 0.116

Gnomad4 NFE AF: 0.0591

Gnomad4 OTH AF: 0.0318

Alfa AF: 0.0329 Hom.: 35

Bravo AF: 0.0337

Asia WGS AF: 0.00577 AC: 20 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.4
DANN	Benign	0.49

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: rs10497109; hg19: chr2-153438591;