rs6597007

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -4.21

Publications

15 publications found
Variant links:
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]

Genome browser will be placed here

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
FAM50BNM_012135.3 linkc.*170C>G 3_prime_UTR_variant Exon 2 of 2 ENST00000648326.1 NP_036267.1 Q9Y247A0A024QZY3
FAM50BXM_017010729.2 linkc.*170C>G 3_prime_UTR_variant Exon 2 of 2 XP_016866218.1 Q9Y247A0A024QZY3

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
FAM50BENST00000648326.1 linkc.*170C>G 3_prime_UTR_variant Exon 2 of 2 NM_012135.3 ENSP00000496837.1 Q9Y247

Frequencies

GnomAD3 genomes
AF:
0.154
AC:
23456
AN:
152062
Hom.:
2134
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.251
Gnomad AMI
AF:
0.0450
Gnomad AMR
AF:
0.0992
Gnomad ASJ
AF:
0.118
Gnomad EAS
AF:
0.221
Gnomad SAS
AF:
0.100
Gnomad FIN
AF:
0.106
Gnomad MID
AF:
0.158
Gnomad NFE
AF:
0.117
Gnomad OTH
AF:
0.145
GnomAD4 exome
AF:
0.122
AC:
120250
AN:
986712
Hom.:
7862
Cov.:
13
AF XY:
0.121
AC XY:
59123
AN XY:
488632
show subpopulations
African (AFR)
AF:
0.264
AC:
5862
AN:
22212
American (AMR)
AF:
0.0840
AC:
1625
AN:
19340
Ashkenazi Jewish (ASJ)
AF:
0.109
AC:
1847
AN:
16914
East Asian (EAS)
AF:
0.202
AC:
6689
AN:
33178
South Asian (SAS)
AF:
0.106
AC:
5922
AN:
56038
European-Finnish (FIN)
AF:
0.102
AC:
4478
AN:
44036
Middle Eastern (MID)
AF:
0.141
AC:
428
AN:
3040
European-Non Finnish (NFE)
AF:
0.117
AC:
87673
AN:
748860
Other (OTH)
AF:
0.133
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

Age Distribution

Exome Het
Exome Hom
Variant carriers
0
3102
6204
9306
12408
15510
<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:
0.154
AC:
23472
AN:
152180
Hom.:
2137
Cov.:
33
AF XY:
0.152
AC XY:
11325
AN XY:
74396
show subpopulations
African (AFR)
AF:
0.251
AC:
10422
AN:
41470
American (AMR)
AF:
0.0990
AC:
1514
AN:
15296
Ashkenazi Jewish (ASJ)
AF:
0.118
AC:
408
AN:
3472
East Asian (EAS)
AF:
0.221
AC:
1144
AN:
5174
South Asian (SAS)
AF:
0.100
AC:
484
AN:
4818
European-Finnish (FIN)
AF:
0.106
AC:
1119
AN:
10604
Middle Eastern (MID)
AF:
0.156
AC:
46
AN:
294
European-Non Finnish (NFE)
AF:
0.117
AC:
7991
AN:
68024
Other (OTH)
AF:
0.143
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

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
244
488
732
976
1220
<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:
0.120
Hom.:
182
Bravo
AF:
0.160
Asia WGS
AF:
0.137
AC:
479
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
0.085
DANN
Benign
0.43
PhyloP100
-4.2
Mutation Taster
=100/0
polymorphism (auto)

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs6597007; hg19: chr6-3851193; API