2-152624531-A-G

Variant names:

• chr2-152624531-A-G
• rs3845678
• NM_052905.4:c.1838-907A>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.1838-907A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.673 in 151,158 control chromosomes in the GnomAD database, including 34,365 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 0.67 (34365 hom., cov: 29)
• Consequence: FMNL2 NM_052905.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.58
• Publications: 1 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=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.832 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FMNL2	NM_052905.4	MANE Select	c.1838-907A>G		intron	N/A	NP_443137.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FMNL2	ENST00000288670.14	TSL:1 MANE Select	c.1838-907A>G		intron	N/A	ENSP00000288670.9	Q96PY5-3
	FMNL2	ENST00000475377.3	TSL:5	c.1859-907A>G		intron	N/A	ENSP00000418959.3	C9IZY8
	FMNL2	ENST00000850952.1		c.1838-907A>G		intron	N/A	ENSP00000521036.1	A0ABJ7H8L6

Frequencies

GnomAD3 genomes AF: 0.673 AC: 101577 AN: 151042 Hom.: 34339 Cov.: 29

Gnomad AFR AF: 0.690

Gnomad AMI AF: 0.770

Gnomad AMR AF: 0.672

Gnomad ASJ AF: 0.674

Gnomad EAS AF: 0.853

Gnomad SAS AF: 0.677

Gnomad FIN AF: 0.774

Gnomad MID AF: 0.728

Gnomad NFE AF: 0.630

Gnomad OTH AF: 0.690

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

GnomAD4 genome AF: 0.673 AC: 101659 AN: 151158 Hom.: 34365 Cov.: 29 AF XY: 0.680 AC XY: 50238 AN XY: 73870

African (AFR) AF: 0.690 AC: 28400 AN: 41154

American (AMR) AF: 0.672 AC: 10231 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.674 AC: 2335 AN: 3462

East Asian (EAS) AF: 0.853 AC: 4354 AN: 5104

South Asian (SAS) AF: 0.677 AC: 3234 AN: 4776

European-Finnish (FIN) AF: 0.774 AC: 8103 AN: 10472

Middle Eastern (MID) AF: 0.721 AC: 209 AN: 290

European-Non Finnish (NFE) AF: 0.630 AC: 42647 AN: 67666

Other (OTH) AF: 0.687 AC: 1445 AN: 2104

Alfa AF: 0.645 Hom.: 3939

Bravo AF: 0.669

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.86
DANN	Benign	0.24
PhyloP100		-1.6
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: rs3845678; hg19: chr2-153481045;