Variant rs61746445 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The ENST00000265018.4(FAM184B):c.199C>T(p.Arg67Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00264 in 1,545,308 control chromosomes in the GnomAD database, including 16 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0020 ( 1 hom., cov: 33)

Exomes 𝑓: 0.0027 ( 15 hom. )

Consequence

FAM184B
ENST00000265018.4 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.89

Variant links:

Genes affected

FAM184B (HGNC:29235): (family with sequence similarity 184 member B)

FAM184B links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.006183207).

BP6

Variant 4-17709587-G-A is Benign according to our data. Variant chr4-17709587-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2654690.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAdExome4 at 15 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FAM184B	NM_015688.2 linkuse as main transcript	c.199C>T	p.Arg67Trp	missense_variant	2/18	ENST00000265018.4	NP_056503.1
FAM184B	XM_047450066.1 linkuse as main transcript	c.199C>T	p.Arg67Trp	missense_variant	2/17		XP_047306022.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FAM184B	ENST00000265018.4 linkuse as main transcript	c.199C>T	p.Arg67Trp	missense_variant	2/18	1	NM_015688.2	ENSP00000265018	P1

Frequencies

GnomAD3 genomes

AF:

0.00202

AC:

307

AN:

152222

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000362

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00164

Gnomad ASJ

AF:

0.00634

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00414

Gnomad FIN

AF:

0.000565

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00317

Gnomad OTH

AF:

0.00144

GnomAD3 exomes

AF:

0.00254

AC:

364

AN:

143202

Hom.:

AF XY:

0.00268

AC XY:

206

AN XY:

76752

show subpopulations

Gnomad AFR exome

AF:

0.000293

Gnomad AMR exome

AF:

0.000902

Gnomad ASJ exome

AF:

0.00762

Gnomad EAS exome

AF:

0.0000956

Gnomad SAS exome

AF:

0.00386

Gnomad FIN exome

AF:

0.000743

Gnomad NFE exome

AF:

0.00307

Gnomad OTH exome

AF:

0.00490

GnomAD4 exome

AF:

0.00271

AC:

3775

AN:

1392968

Hom.:

Cov.:

AF XY:

0.00282

AC XY:

1935

AN XY:

686998

show subpopulations

Gnomad4 AFR exome

AF:

0.000415

Gnomad4 AMR exome

AF:

0.00103

Gnomad4 ASJ exome

AF:

0.00801

Gnomad4 EAS exome

AF:

0.0000280

Gnomad4 SAS exome

AF:

0.00383

Gnomad4 FIN exome

AF:

0.000914

Gnomad4 NFE exome

AF:

0.00269

Gnomad4 OTH exome

AF:

0.00388

GnomAD4 genome

AF:

0.00202

AC:

307

AN:

152340

Hom.:

Cov.:

AF XY:

0.00201

AC XY:

150

AN XY:

74490

show subpopulations

Gnomad4 AFR

AF:

0.000361

Gnomad4 AMR

AF:

0.00163

Gnomad4 ASJ

AF:

0.00634

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00414

Gnomad4 FIN

AF:

0.000565

Gnomad4 NFE

AF:

0.00317

Gnomad4 OTH

AF:

0.00142

Alfa

AF:

0.00305

Hom.:

Bravo

AF:

0.00211

TwinsUK

AF:

0.00189

AC:

ALSPAC

AF:

0.00234

AC:

ExAC

AF:

0.00240

AC:

Asia WGS

AF:

0.00173

AC:

AN:

3478

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

Nov 01, 2022

FAM184B: BP4, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.13

BayesDel_addAF

Benign

-0.24

BayesDel_noAF

Benign

-0.11

CADD

Benign

DANN

Uncertain

1.0

DEOGEN2

Benign

0.34

Eigen

Benign

0.044

Eigen_PC

Benign

-0.11

FATHMM_MKL

Benign

0.47

LIST_S2

Uncertain

0.87

M_CAP

Uncertain

0.18

MetaRNN

Benign

0.0062

MetaSVM

Benign

-0.46

MutationAssessor

Uncertain

2.2

MutationTaster

Benign

1.0

PrimateAI

Benign

0.48

PROVEAN

Pathogenic

-5.0

REVEL

Uncertain

0.37

Sift

Uncertain

0.0010

Sift4G

Uncertain

0.0040

Polyphen

1.0

Vest4

0.27

MVP

0.36

ClinPred

0.045

GERP RS

1.1

Varity_R

0.34

gMVP

0.41

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

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