Variant rs61742285 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2

The NM_015688.2(FAM184B):c.2659G>C(p.Glu887Gln) variant causes a missense change. The variant allele was found at a frequency of 0.0224 in 1,551,624 control chromosomes in the GnomAD database, including 500 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.015 ( 29 hom., cov: 32)

Exomes 𝑓: 0.023 ( 471 hom. )

Consequence

FAM184B
NM_015688.2 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 5.32

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 -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0059881806).

BS1

Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0152 (2313/152326) while in subpopulation NFE AF= 0.0253 (1722/68026). AF 95% confidence interval is 0.0243. There are 29 homozygotes in gnomad4. There are 1026 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 29 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FAM184B	NM_015688.2 linkuse as main transcript	c.2659G>C	p.Glu887Gln	missense_variant	14/18	ENST00000265018.4	NP_056503.1	Q9ULE4
FAM184B	XM_047450066.1 linkuse as main transcript	c.2659G>C	p.Glu887Gln	missense_variant	14/17		XP_047306022.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FAM184B	ENST00000265018.4 linkuse as main transcript	c.2659G>C	p.Glu887Gln	missense_variant	14/18	1	NM_015688.2	ENSP00000265018.3		Q9ULE4

Frequencies

GnomAD3 genomes

AF:

0.0152

AC:

2312

AN:

152208

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00480

Gnomad AMI

AF:

0.0537

Gnomad AMR

AF:

0.00917

Gnomad ASJ

AF:

0.0141

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00331

Gnomad FIN

AF:

0.0105

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0253

Gnomad OTH

AF:

0.0124

GnomAD3 exomes

AF:

0.0134

AC:

2081

AN:

155872

Hom.:

AF XY:

0.0135

AC XY:

1115

AN XY:

82686

show subpopulations

Gnomad AFR exome

AF:

0.00356

Gnomad AMR exome

AF:

0.00664

Gnomad ASJ exome

AF:

0.0134

Gnomad EAS exome

AF:

0.0000918

Gnomad SAS exome

AF:

0.00360

Gnomad FIN exome

AF:

0.0107

Gnomad NFE exome

AF:

0.0241

Gnomad OTH exome

AF:

0.0146

GnomAD4 exome

AF:

0.0232

AC:

32497

AN:

1399298

Hom.:

471

Cov.:

AF XY:

0.0225

AC XY:

15547

AN XY:

690156

show subpopulations

Gnomad4 AFR exome

AF:

0.00304

Gnomad4 AMR exome

AF:

0.00667

Gnomad4 ASJ exome

AF:

0.0131

Gnomad4 EAS exome

AF:

0.0000839

Gnomad4 SAS exome

AF:

0.00380

Gnomad4 FIN exome

AF:

0.0123

Gnomad4 NFE exome

AF:

0.0278

Gnomad4 OTH exome

AF:

0.0164

GnomAD4 genome

AF:

0.0152

AC:

2313

AN:

152326

Hom.:

Cov.:

AF XY:

0.0138

AC XY:

1026

AN XY:

74488

show subpopulations

Gnomad4 AFR

AF:

0.00479

Gnomad4 AMR

AF:

0.00916

Gnomad4 ASJ

AF:

0.0141

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00331

Gnomad4 FIN

AF:

0.0105

Gnomad4 NFE

AF:

0.0253

Gnomad4 OTH

AF:

0.0123

Alfa

AF:

0.0221

Hom.:

Bravo

AF:

0.0146

TwinsUK

AF:

0.0254

AC:

ALSPAC

AF:

0.0298

AC:

115

ESP6500AA

AF:

0.00361

AC:

ESP6500EA

AF:

0.0264

AC:

ExAC

AF:

0.00971

AC:

249

Asia WGS

AF:

0.000577

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.14

BayesDel_addAF

Benign

-0.45

BayesDel_noAF

Benign

-0.38

CADD

Uncertain

DANN

Uncertain

1.0

DEOGEN2

Benign

0.080

Eigen

Uncertain

0.37

Eigen_PC

Uncertain

0.40

FATHMM_MKL

Uncertain

0.91

LIST_S2

Benign

0.78

MetaRNN

Benign

0.0060

MetaSVM

Benign

-1.1

MutationAssessor

Benign

1.7

PrimateAI

Uncertain

0.56

PROVEAN

Benign

-0.34

REVEL

Benign

0.20

Sift

Benign

0.72

Sift4G

Uncertain

0.030

Polyphen

1.0

Vest4

0.47

ClinPred

0.014

GERP RS

5.0

Varity_R

0.22

gMVP

0.18

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over