rs61742285
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_015688.2(FAM184B):āc.2659G>Cā(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: š 0.015 ( 29 hom., cov: 32)
Exomes š: 0.023 ( 471 hom. )
Consequence
FAM184B
NM_015688.2 missense
NM_015688.2 missense
Scores
6
12
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 5.32
Genes affected
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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 | UniProt |
---|---|---|---|---|---|---|---|
FAM184B | NM_015688.2 | c.2659G>C | p.Glu887Gln | missense_variant | 14/18 | ENST00000265018.4 | |
FAM184B | XM_047450066.1 | c.2659G>C | p.Glu887Gln | missense_variant | 14/17 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FAM184B | ENST00000265018.4 | c.2659G>C | p.Glu887Gln | missense_variant | 14/18 | 1 | NM_015688.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0152 AC: 2312AN: 152208Hom.: 29 Cov.: 32
GnomAD3 genomes
?
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GnomAD3 exomes AF: 0.0134 AC: 2081AN: 155872Hom.: 27 AF XY: 0.0135 AC XY: 1115AN XY: 82686
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GnomAD4 exome AF: 0.0232 AC: 32497AN: 1399298Hom.: 471 Cov.: 34 AF XY: 0.0225 AC XY: 15547AN XY: 690156
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GnomAD4 genome ? AF: 0.0152 AC: 2313AN: 152326Hom.: 29 Cov.: 32 AF XY: 0.0138 AC XY: 1026AN XY: 74488
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94
ALSPAC
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115
ESP6500AA
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ESP6500EA
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84
ExAC
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249
Asia WGS
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3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Benign
T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Benign
L
MutationTaster
Benign
D
PrimateAI
Uncertain
T
PROVEAN
Benign
N
REVEL
Benign
Sift
Benign
T
Sift4G
Uncertain
D
Polyphen
D
Vest4
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at