rs183796305

Variant names:

Your query was ambiguous. Multiple possible variants found:

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_ModerateBP6_ModerateBS2

The NM_001388459.1(FRMPD3):c.290C>G(p.Thr97Ser) variant causes a missense change. The variant allele was found at a frequency of 0.0000639 in 1,204,730 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 20 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 12/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.000062 ( 0 hom., 1 hem., cov: 23)

Exomes 𝑓: 0.000064 ( 0 hom. 19 hem. )

Consequence

FRMPD3
NM_001388459.1 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 4.59

Publications

1 publications found

Variant links:

Genes affected

FRMPD3 (HGNC:29382): (FERM and PDZ domain containing 3) This gene encodes a protein that contains a PDZ (post synaptic density protein (PSD95), Drosophila disc large tumor suppressor (Dlg1), and zonula occludens-1 protein (zo-1) domain at the N-terminus followed by a FERM domain. The encoded protein is involved in signal transduction. The PDZ domain is thought to function in protein-protein interactions, mainly by binding to specific C-terminal peptides of other proteins. The FERM domain is found in proteins that are localized to the plasma membrane and are associated with the cytoskeleton. [provided by RefSeq, May 2017]

FRMPD3 links:

FRMPD3-AS1 (HGNC:41239): (FRMPD3 antisense RNA 1)

FRMPD3-AS1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -8 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.102440596).

BP6

Variant X-107533543-C-G is Benign according to our data. Variant chrX-107533543-C-G is described in ClinVar as Likely_benign. ClinVar VariationId is 2661145.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Hemizygotes in GnomAdExome4 at 19 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001388459.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
FRMPD3	NM_001388459.1	MANE Select	c.290C>G	p.Thr97Ser	missense	Exon 4 of 15	NP_001375388.1	Q5JV73
FRMPD3	NM_032428.2		c.389C>G	p.Thr130Ser	missense	Exon 5 of 16	NP_115804.1
FRMPD3	NM_001388462.1		c.-109+3032C>G		intron	N/A	NP_001375391.1	A0A804HJA6

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
FRMPD3	ENST00000683843.1	MANE Select	c.290C>G	p.Thr97Ser	missense	Exon 4 of 15	ENSP00000507942.1	Q5JV73
FRMPD3	ENST00000276185.9	TSL:5	c.290C>G	p.Thr97Ser	missense	Exon 5 of 16	ENSP00000276185.5	Q5JV73
FRMPD3	ENST00000439554.1	TSL:5	c.233C>G	p.Thr78Ser	missense	Exon 3 of 14	ENSP00000398668.1	A0A0A0MSP7

Frequencies

GnomAD3 genomes

AF:

0.0000624

AC:

AN:

112182

Hom.:

Cov.:

show subpopulations

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:

0.000131

Gnomad OTH

AF:

0.00

GnomAD2 exomes

AF:

0.0000820

AC:

AN:

170810

AF XY:

0.0000642

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.0000379

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000173

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.0000641

AC:

AN:

1092495

Hom.:

Cov.:

AF XY:

0.0000530

AC XY:

AN XY:

358717

show subpopulations

African (AFR)

AF:

0.0000761

AC:

AN:

26295

American (AMR)

AF:

0.0000286

AC:

AN:

34958

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

19339

East Asian (EAS)

AF:

0.00

AC:

AN:

30117

South Asian (SAS)

AF:

0.00

AC:

AN:

53491

European-Finnish (FIN)

AF:

0.00

AC:

AN:

39435

Middle Eastern (MID)

AF:

0.00

AC:

AN:

4120

European-Non Finnish (NFE)

AF:

0.0000787

AC:

AN:

838807

Other (OTH)

AF:

0.0000218

AC:

AN:

45933

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.454

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0000624

AC:

AN:

112235

Hom.:

Cov.:

AF XY:

0.0000291

AC XY:

AN XY:

34391

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

30911

American (AMR)

AF:

0.00

AC:

AN:

10574

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

2652

East Asian (EAS)

AF:

0.00

AC:

AN:

3572

South Asian (SAS)

AF:

0.00

AC:

AN:

2679

European-Finnish (FIN)

AF:

0.00

AC:

AN:

6175

Middle Eastern (MID)

AF:

0.00

AC:

AN:

219

European-Non Finnish (NFE)

AF:

0.000131

AC:

AN:

53239

Other (OTH)

AF:

0.00

AC:

AN:

1526

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0000712

Hom.:

Bravo

AF:

0.0000680

ESP6500AA

AF:

0.00

AC:

ESP6500EA

AF:

0.000644

AC:

ExAC

AF:

0.0000603

AC:

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

AlphaMissense

Benign

0.12

BayesDel_addAF

Benign

-0.35

BayesDel_noAF

Benign

-0.49

CADD

Benign

(source)

DANN

Benign

0.95

DEOGEN2

Benign

0.014

FATHMM_MKL

Uncertain

0.96

LIST_S2

Benign

0.55

M_CAP

Uncertain

0.23

MetaRNN

Benign

0.10

MetaSVM

Benign

-0.85

MutationAssessor

Benign

0.55

PhyloP100

4.6

PROVEAN

Benign

-1.4

REVEL

Benign

0.042

Sift

Benign

0.35

Sift4G

Benign

0.077

Vest4

0.51

MutPred

0.43

Gain of disorder (P = 0.0371)

MVP

0.66

MPC

0.096

ClinPred

0.086

GERP RS

4.6

Varity_R

0.24

gMVP

0.27

Mutation Taster

=100/0

polymorphism

(source)

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over