chr1-240207635-A-T

Variant names:

• chr1-240207635-A-T
• rs188083977
• NM_020066.5:c.2823A>T

Variant summary

Our verdict is Likely benign. The variant received -5 ACMG points: 0P and 5B. BP4_Strong BP7

The NM_020066.5(FMN2):​c.2823A>T​(p.Gly941Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. G941G) has been classified as Likely benign.

• Frequency:
  • Genomes: 𝑓 0.000023 (0 hom., cov: 0)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: FMN2 NM_020066.5 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.845
• Publications: 5 publications found

Genes affected

FMN2 (HGNC:14074): (formin 2) This gene is a member of the formin homology protein family. The encoded protein is thought to have essential roles in organization of the actin cytoskeleton and in cell polarity. This protein mediates the formation of an actin mesh that positions the spindle during oogenesis and also regulates the formation of actin filaments in the nucleus. This protein also forms a perinuclear actin/focal-adhesion system that regulates the shape and position of the nucleus during cell migration. Mutations in this gene have been associated with infertility and also with an autosomal recessive form of intellectual disability (MRT47). Alternatively spliced transcript variants have been identified. [provided by RefSeq, Jul 2017]

FMN2 Gene-Disease associations (from GenCC):

• intellectual disability, autosomal recessive 47

  Inheritance: AR Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics, G2P
• autosomal recessive non-syndromic intellectual disability

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Likely_benign. The variant received -5 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BP7: Synonymous conserved (PhyloP=-0.845 with no splicing effect.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020066.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FMN2	NM_020066.5	MANE Select	c.2823A>T	p.Gly941Gly	synonymous	Exon 5 of 18	NP_064450.3
	FMN2	NM_001305424.2		c.2835A>T	p.Gly945Gly	synonymous	Exon 6 of 19	NP_001292353.1
	FMN2	NM_001348094.2		c.1986+19373A>T		intron	N/A	NP_001335023.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FMN2	ENST00000319653.14	TSL:5 MANE Select	c.2823A>T	p.Gly941Gly	synonymous	Exon 5 of 18	ENSP00000318884.9	Q9NZ56-1
	FMN2	ENST00000679980.1		c.188+643A>T		intron	N/A	ENSP00000505449.1	A0A7P0T994
	FMN2	ENST00000681210.1		c.285+19373A>T		intron	N/A	ENSP00000505131.1	A0A7P0Z432

Frequencies

GnomAD3 genomes AF: 0.0000226 AC: 1 AN: 44266 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000430

Gnomad OTH AF: 0.00

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 868674 Hom.: 0 Cov.: 36 AF XY: 0.00 AC XY: 0 AN XY: 425156

African (AFR) AF: 0.00 AC: 0 AN: 14866

American (AMR) AF: 0.00 AC: 0 AN: 27314

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 8928

East Asian (EAS) AF: 0.00 AC: 0 AN: 12412

South Asian (SAS) AF: 0.00 AC: 0 AN: 43538

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 24718

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1992

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 704680

Other (OTH) AF: 0.00 AC: 0 AN: 30226

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000226 AC: 1 AN: 44266 Hom.: 0 Cov.: 0 AF XY: 0.0000471 AC XY: 1 AN XY: 21232

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.00 AC: 0 AN: 9398

American (AMR) AF: 0.00 AC: 0 AN: 4552

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 820

East Asian (EAS) AF: 0.00 AC: 0 AN: 1372

South Asian (SAS) AF: 0.00 AC: 0 AN: 1258

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2702

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 54

European-Non Finnish (NFE) AF: 0.0000430 AC: 1 AN: 23232

Other (OTH) AF: 0.00 AC: 0 AN: 590

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.61
DANN	Benign	0.30
PhyloP100		-0.84
Mutation Taster		=100/0	polymorphism

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: rs188083977; hg19: chr1-240370935;