Genetic Variant FRG2C:p.Arg163Arg (chr3-75665679-C-A) – ACMG Classification: Benign (-7 pts)

Variant summary

Our verdict is Benign. The variant received -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7

The NM_001124759.5(FRG2C):c.487C>A(p.Arg163Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0 ( 0 hom., cov: 63)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

FRG2C
NM_001124759.5 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.943

Publications

0 publications found

Variant links:

Genes affected

FRG2C (HGNC:33626): (FSHD region gene 2 family member C) Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

FRG2C links:

ENSG00000293315 (HGNC:):

ENSG00000293315 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -7 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BP6

Variant 3-75665679-C-A is Benign according to our data. Variant chr3-75665679-C-A is described in ClinVar as Likely_benign. ClinVar VariationId is 2653973.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-0.943 with no splicing effect.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001124759.5. 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
	FRG2C	NM_001124759.5	MANE Select	c.487C>A	p.Arg163Arg	synonymous	Exon 4 of 4	NP_001118231.1	A6NGY1
	FRG2C	NM_001410775.1		c.484C>A	p.Arg162Arg	synonymous	Exon 4 of 4	NP_001397704.1	C9JUX3

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
FRG2C	ENST00000308062.8	TSL:1 MANE Select	c.487C>A	p.Arg163Arg	synonymous	Exon 4 of 4	ENSP00000312299.3	A6NGY1
FRG2C	ENST00000464571.1	TSL:1	c.484C>A	p.Arg162Arg	synonymous	Exon 4 of 4	ENSP00000419432.1	C9JUX3
ENSG00000293315	ENST00000638439.2	TSL:5	n.185+4341G>T		intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

AN:

149760

Hom.:

Cov.:

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:

0.00

Gnomad OTH

AF:

0.00

GnomAD4 exome

Data not reliable, filtered out with message: AC0;AS_VQSR

AF:

0.00

AC:

AN:

1461638

Hom.:

Cov.:

183

AF XY:

0.00

AC XY:

AN XY:

727136

African (AFR)

AF:

0.00

AC:

AN:

33472

American (AMR)

AF:

0.00

AC:

AN:

44708

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

26130

East Asian (EAS)

AF:

0.00

AC:

AN:

39698

South Asian (SAS)

AF:

0.00

AC:

AN:

86246

European-Finnish (FIN)

AF:

0.00

AC:

AN:

53420

Middle Eastern (MID)

AF:

0.00

AC:

AN:

5762

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

1111826

Other (OTH)

AF:

0.00

AC:

AN:

60376

GnomAD4 genome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

149760

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

73020

African (AFR)

AF:

0.00

AC:

AN:

40686

American (AMR)

AF:

0.00

AC:

AN:

14998

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3432

East Asian (EAS)

AF:

0.00

AC:

AN:

5014

South Asian (SAS)

AF:

0.00

AC:

AN:

4688

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10406

Middle Eastern (MID)

AF:

0.00

AC:

AN:

312

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

67288

Other (OTH)

AF:

0.00

AC:

AN:

2044

ClinVar

ClinVar submissions

Significance:Likely benign

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

4.1

(source)

DANN

Benign

0.75

PhyloP100

-0.94

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over