rs61746992

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_StrongBS2

The NM_015688.2(FAM184B):​c.823G>C​(p.Asp275His) variant causes a missense change. The variant allele was found at a frequency of 0.00526 in 1,550,388 control chromosomes in the GnomAD database, including 37 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 0.0032 ( 6 hom., cov: 29)
Exomes 𝑓: 0.0055 ( 31 hom. )

Consequence

FAM184B
NM_015688.2 missense

Scores

3
10
6

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 6.78
Variant links:
Genes affected
FAM184B (HGNC:29235): (family with sequence similarity 184 member B)

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=0.010471642).
BS2
High Homozygotes in GnomAd4 at 6 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
FAM184BNM_015688.2 linkc.823G>C p.Asp275His missense_variant Exon 2 of 18 ENST00000265018.4 NP_056503.1 Q9ULE4
FAM184BXM_047450066.1 linkc.823G>C p.Asp275His missense_variant Exon 2 of 17 XP_047306022.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
FAM184BENST00000265018.4 linkc.823G>C p.Asp275His missense_variant Exon 2 of 18 1 NM_015688.2 ENSP00000265018.3 Q9ULE4

Frequencies

GnomAD3 genomes
AF:
0.00323
AC:
491
AN:
151916
Hom.:
6
Cov.:
29
show subpopulations
Gnomad AFR
AF:
0.000895
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00302
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00145
Gnomad FIN
AF:
0.000755
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00574
Gnomad OTH
AF:
0.00144
GnomAD2 exomes
AF:
0.00293
AC:
455
AN:
155496
AF XY:
0.00294
show subpopulations
Gnomad AFR exome
AF:
0.000632
Gnomad AMR exome
AF:
0.00276
Gnomad ASJ exome
AF:
0.000119
Gnomad EAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.000485
Gnomad NFE exome
AF:
0.00538
Gnomad OTH exome
AF:
0.00298
GnomAD4 exome
AF:
0.00548
AC:
7668
AN:
1398352
Hom.:
31
Cov.:
30
AF XY:
0.00534
AC XY:
3685
AN XY:
689660
show subpopulations
Gnomad4 AFR exome
AF:
0.000633
AC:
20
AN:
31588
Gnomad4 AMR exome
AF:
0.00320
AC:
114
AN:
35666
Gnomad4 ASJ exome
AF:
0.0000797
AC:
2
AN:
25088
Gnomad4 EAS exome
AF:
0.0000280
AC:
1
AN:
35736
Gnomad4 SAS exome
AF:
0.00207
AC:
164
AN:
79116
Gnomad4 FIN exome
AF:
0.000573
AC:
28
AN:
48874
Gnomad4 NFE exome
AF:
0.00655
AC:
7063
AN:
1078624
Gnomad4 Remaining exome
AF:
0.00464
AC:
269
AN:
57972
Heterozygous variant carriers
0
470
940
1410
1880
2350
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Exome Het
Exome Hom
Variant carriers
0
282
564
846
1128
1410
<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:
0.00322
AC:
490
AN:
152036
Hom.:
6
Cov.:
29
AF XY:
0.00293
AC XY:
218
AN XY:
74300
show subpopulations
Gnomad4 AFR
AF:
0.000892
AC:
0.000892125
AN:
0.000892125
Gnomad4 AMR
AF:
0.00301
AC:
0.00301284
AN:
0.00301284
Gnomad4 ASJ
AF:
0.00
AC:
0
AN:
0
Gnomad4 EAS
AF:
0.00
AC:
0
AN:
0
Gnomad4 SAS
AF:
0.00145
AC:
0.00145108
AN:
0.00145108
Gnomad4 FIN
AF:
0.000755
AC:
0.000755002
AN:
0.000755002
Gnomad4 NFE
AF:
0.00572
AC:
0.00572328
AN:
0.00572328
Gnomad4 OTH
AF:
0.00143
AC:
0.00142586
AN:
0.00142586
Heterozygous variant carriers
0
27
54
81
108
135
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Genome Het
Genome Hom
Variant carriers
0
10
20
30
40
50
<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:
0.00416
Hom.:
2
Bravo
AF:
0.00360
TwinsUK
AF:
0.0111
AC:
41
ALSPAC
AF:
0.00623
AC:
24
ESP6500AA
AF:
0.00
AC:
0
ESP6500EA
AF:
0.00409
AC:
13
ExAC
AF:
0.00145
AC:
44

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.63
BayesDel_addAF
Benign
-0.14
T
BayesDel_noAF
Uncertain
0.040
CADD
Pathogenic
27
DANN
Uncertain
1.0
DEOGEN2
Benign
0.27
T
Eigen
Pathogenic
0.69
Eigen_PC
Pathogenic
0.66
FATHMM_MKL
Uncertain
0.91
D
LIST_S2
Benign
0.81
T
M_CAP
Benign
0.062
D
MetaRNN
Benign
0.010
T
MetaSVM
Uncertain
0.23
D
MutationAssessor
Uncertain
2.5
M
PrimateAI
Uncertain
0.58
T
PROVEAN
Uncertain
-4.1
D
REVEL
Uncertain
0.44
Sift
Uncertain
0.0030
D
Sift4G
Uncertain
0.012
D
Polyphen
1.0
D
Vest4
0.31
MVP
0.35
ClinPred
0.022
T
GERP RS
5.1
Varity_R
0.67
gMVP
0.33
Mutation Taster
=96/4
polymorphism

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.

Other links and lift over

dbSNP: rs61746992; hg19: chr4-17710586; COSMIC: COSV105872416; API