chr2-152619552-G-GCCA

Position:

• chr2-152619552-G-GCCA

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP6_Moderate

The NM_052905.4(FMNL2):​c.1673_1674insACC​(p.Pro572dup) variant causes a inframe insertion change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.99 (58402 hom., cov: 0)
  • Exomes 𝑓: 0.98 (617223 hom.)
  • Failed GnomAD Quality Control
• Consequence: FMNL2 NM_052905.4 inframe_insertion
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.14

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 Likely_benign. Variant got -2 ACMG points.

• BP6: Variant 2-152619552-G-GCCA is Benign according to our data. Variant chr2-152619552-G-GCCA is described in ClinVar as [Benign]. Clinvar id is 3060523.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FMNL2	NM_052905.4	c.1673_1674insACC	p.Pro572dup	inframe_insertion	15/26	ENST00000288670.14

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FMNL2	ENST00000288670.14	c.1673_1674insACC	p.Pro572dup	inframe_insertion	15/26	1	NM_052905.4	P1
FMNL2	ENST00000475377.3	c.1673_1674insACC	p.Pro572dup	inframe_insertion	15/28	5

Frequencies

GnomAD3 genomes AF: 0.00 AC: 117855 AN: 119010 Hom.: 58352 Cov.: 0 FAILED QC

Gnomad AFR AF: 0.983

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.985

Gnomad ASJ AF: 0.998

Gnomad EAS AF: 0.982

Gnomad SAS AF: 0.992

Gnomad FIN AF: 0.991

Gnomad MID AF: 0.993

Gnomad NFE AF: 0.995

Gnomad OTH AF: 0.987

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.975 AC: 1266615 AN: 1298848 Hom.: 617223 Cov.: 36 AF XY: 0.974 AC XY: 625013 AN XY: 641532

Gnomad4 AFR exome AF: 0.972

Gnomad4 AMR exome AF: 0.966

Gnomad4 ASJ exome AF: 0.972

Gnomad4 EAS exome AF: 0.950

Gnomad4 SAS exome AF: 0.956

Gnomad4 FIN exome AF: 0.958

Gnomad4 NFE exome AF: 0.979

Gnomad4 OTH exome AF: 0.970

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.990 AC: 117961 AN: 119122 Hom.: 58402 Cov.: 0 AF XY: 0.990 AC XY: 55854 AN XY: 56438

Gnomad4 AFR AF: 0.983

Gnomad4 AMR AF: 0.985

Gnomad4 ASJ AF: 0.998

Gnomad4 EAS AF: 0.982

Gnomad4 SAS AF: 0.992

Gnomad4 FIN AF: 0.991

Gnomad4 NFE AF: 0.995

Gnomad4 OTH AF: 0.987

Alfa AF: 0.949 Hom.: 6507

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

FMNL2-related disorder Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

Apr 26, 2023

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs5835439; hg19: chr2-153476066;