12-124314355-GC-G

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_001365156.1(RFLNA):c.484del(p.Leu162CysfsTer111) variant causes a frameshift change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (no stars).

• Frequency: Genomes: not found (cov: 33)
• Consequence: RFLNA NM_001365156.1 frameshift
• Clinical Significance: Uncertain significance no assertion criteria provided U:1
• Conservation: PhyloP100: 7.44

Genes affected

RFLNA (HGNC:27051): (refilin A) Predicted to enable filamin binding activity. Predicted to be involved in several processes, including actin filament bundle organization; negative regulation of bone mineralization involved in bone maturation; and negative regulation of chondrocyte development. Predicted to be located in cytoplasm. Predicted to be active in actin filament bundle. [provided by Alliance of Genome Resources, Apr 2022]

ZNF664-RFLNA (HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RFLNA	NM_001365156.1	c.484del	p.Leu162CysfsTer111	frameshift_variant	3/3	ENST00000546355.4
ZNF664-RFLNA	NM_001204299.3	c.241del	p.Leu81CysfsTer111	frameshift_variant	5/5
ZNF664-RFLNA	NM_001347902.2	c.241del	p.Leu81CysfsTer111	frameshift_variant	5/5
RFLNA	NM_181709.5	c.241del	p.Leu81CysfsTer111	frameshift_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RFLNA	ENST00000546355.4	c.484del	p.Leu162CysfsTer111	frameshift_variant	3/3	1	NM_001365156.1	P1
RFLNA	ENST00000338359.4	c.241del	p.Leu81CysfsTer?	frameshift_variant	2/2	1
RFLNA	ENST00000324038.6	c.241del	p.Leu81CysfsTer111	frameshift_variant	3/3	2
RFLNA	ENST00000389727.8	c.241del	p.Leu81CysfsTer111	frameshift_variant	5/5	5

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 33

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: no assertion criteria provided

Submissions by phenotype

not provided Uncertain:1

Uncertain significance, no assertion criteria provided

literature only

OMIM

Dec 20, 2021

- -

Computational scores

Source: dbNSFP v4.3

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr12-124798901;