rs6597007
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_012135.3(FAM50B):c.*170C>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.126 in 1,138,892 control chromosomes in the GnomAD database, including 9,999 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 0.15 ( 2137 hom., cov: 33)
Exomes 𝑓: 0.12 ( 7862 hom. )
Consequence
FAM50B
NM_012135.3 3_prime_UTR
NM_012135.3 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -4.21
Publications
15 publications found
Genes affected
FAM50B (HGNC:18789): (family with sequence similarity 50 member B) This gene contains an intronless ORF that arose from ancestral retroposition. The encoded protein is related to a plant protein that plays a role in the circadian clock. This gene is adjacent to a differentially methylated region (DMR) and is imprinted and paternally expressed in many tissues. [provided by RefSeq, Nov 2015]
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ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.247 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FAM50B | NM_012135.3 | c.*170C>G | 3_prime_UTR_variant | Exon 2 of 2 | ENST00000648326.1 | NP_036267.1 | ||
FAM50B | XM_017010729.2 | c.*170C>G | 3_prime_UTR_variant | Exon 2 of 2 | XP_016866218.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.154 AC: 23456AN: 152062Hom.: 2134 Cov.: 33 show subpopulations
GnomAD3 genomes
AF:
AC:
23456
AN:
152062
Hom.:
Cov.:
33
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.122 AC: 120250AN: 986712Hom.: 7862 Cov.: 13 AF XY: 0.121 AC XY: 59123AN XY: 488632 show subpopulations
GnomAD4 exome
AF:
AC:
120250
AN:
986712
Hom.:
Cov.:
13
AF XY:
AC XY:
59123
AN XY:
488632
show subpopulations
African (AFR)
AF:
AC:
5862
AN:
22212
American (AMR)
AF:
AC:
1625
AN:
19340
Ashkenazi Jewish (ASJ)
AF:
AC:
1847
AN:
16914
East Asian (EAS)
AF:
AC:
6689
AN:
33178
South Asian (SAS)
AF:
AC:
5922
AN:
56038
European-Finnish (FIN)
AF:
AC:
4478
AN:
44036
Middle Eastern (MID)
AF:
AC:
428
AN:
3040
European-Non Finnish (NFE)
AF:
AC:
87673
AN:
748860
Other (OTH)
AF:
AC:
5726
AN:
43094
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.508
Heterozygous variant carriers
0
5211
10422
15633
20844
26055
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome AF: 0.154 AC: 23472AN: 152180Hom.: 2137 Cov.: 33 AF XY: 0.152 AC XY: 11325AN XY: 74396 show subpopulations
GnomAD4 genome
AF:
AC:
23472
AN:
152180
Hom.:
Cov.:
33
AF XY:
AC XY:
11325
AN XY:
74396
show subpopulations
African (AFR)
AF:
AC:
10422
AN:
41470
American (AMR)
AF:
AC:
1514
AN:
15296
Ashkenazi Jewish (ASJ)
AF:
AC:
408
AN:
3472
East Asian (EAS)
AF:
AC:
1144
AN:
5174
South Asian (SAS)
AF:
AC:
484
AN:
4818
European-Finnish (FIN)
AF:
AC:
1119
AN:
10604
Middle Eastern (MID)
AF:
AC:
46
AN:
294
European-Non Finnish (NFE)
AF:
AC:
7991
AN:
68024
Other (OTH)
AF:
AC:
303
AN:
2116
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
1014
2028
3043
4057
5071
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
479
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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