Variant 22-39995096-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_138435.4(FAM83F):c.54G>A(p.Val18Val) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00713 in 1,356,248 control chromosomes in the GnomAD database, including 59 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0052 ( 2 hom., cov: 32)

Exomes 𝑓: 0.0074 ( 57 hom. )

Consequence

FAM83F
NM_138435.4 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.430

Variant links:

Genes affected

FAM83F (HGNC:25148): (family with sequence similarity 83 member F) Predicted to enable protein kinase binding activity. Predicted to be involved in signal transduction. [provided by Alliance of Genome Resources, Apr 2022]

FAM83F links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.5).

BP6

Variant 22-39995096-G-A is Benign according to our data. Variant chr22-39995096-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2653166.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=0.43 with no splicing effect.

BS2

High Homozygotes in GnomAd4 at 2 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FAM83F	NM_138435.4 linkuse as main transcript	c.54G>A	p.Val18Val	synonymous_variant	1/5	ENST00000333407.11	NP_612444.2	Q8NEG4-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FAM83F	ENST00000333407.11 linkuse as main transcript	c.54G>A	p.Val18Val	synonymous_variant	1/5	1	NM_138435.4	ENSP00000330432.5		Q8NEG4-1

Frequencies

GnomAD3 genomes

AF:

0.00519

AC:

789

AN:

152012

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00140

Gnomad AMI

AF:

0.0165

Gnomad AMR

AF:

0.00537

Gnomad ASJ

AF:

0.00260

Gnomad EAS

AF:

0.000194

Gnomad SAS

AF:

0.00351

Gnomad FIN

AF:

0.00521

Gnomad MID

AF:

0.00318

Gnomad NFE

AF:

0.00786

Gnomad OTH

AF:

0.00814

GnomAD3 exomes

AF:

0.00510

AC:

AN:

8036

Hom.:

AF XY:

0.00486

AC XY:

AN XY:

4528

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00408

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00372

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00779

Gnomad OTH exome

AF:

0.00431

GnomAD4 exome

AF:

0.00738

AC:

8883

AN:

1204128

Hom.:

Cov.:

AF XY:

0.00728

AC XY:

4243

AN XY:

582476

show subpopulations

Gnomad4 AFR exome

AF:

0.00111

Gnomad4 AMR exome

AF:

0.00435

Gnomad4 ASJ exome

AF:

0.00308

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00338

Gnomad4 FIN exome

AF:

0.00632

Gnomad4 NFE exome

AF:

0.00814

Gnomad4 OTH exome

AF:

0.00567

GnomAD4 genome

AF:

0.00519

AC:

789

AN:

152120

Hom.:

Cov.:

AF XY:

0.00523

AC XY:

389

AN XY:

74354

show subpopulations

Gnomad4 AFR

AF:

0.00140

Gnomad4 AMR

AF:

0.00536

Gnomad4 ASJ

AF:

0.00260

Gnomad4 EAS

AF:

0.000194

Gnomad4 SAS

AF:

0.00352

Gnomad4 FIN

AF:

0.00521

Gnomad4 NFE

AF:

0.00786

Gnomad4 OTH

AF:

0.00806

Alfa

AF:

0.00545

Hom.:

Bravo

AF:

0.00484

Asia WGS

AF:

0.00233

AC:

AN:

3450

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Jul 01, 2022

FAM83F: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.50

CADD

Benign

DANN

Benign

0.97

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.060

Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over