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12-13061603-A-G

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1

The NM_020853.2(FAM234B):c.561A>G(p.Val187=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.814 in 1,612,674 control chromosomes in the GnomAD database, including 542,590 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.73 ( 41896 hom., cov: 31)
Exomes 𝑓: 0.82 ( 500694 hom. )

Consequence

FAM234B
NM_020853.2 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.859
Variant links:
Genes affected
FAM234B (HGNC:29288): (family with sequence similarity 234 member B) Predicted to be located in Golgi apparatus and cytoskeleton. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.55).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 12-13061603-A-G is Benign according to our data. Variant chr12-13061603-A-G is described in ClinVar as [Benign]. Clinvar id is 3060677.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=0.859 with no splicing effect.
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.852 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
FAM234BNM_020853.2 linkuse as main transcriptc.561A>G p.Val187= synonymous_variant 4/13 ENST00000197268.13

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
FAM234BENST00000197268.13 linkuse as main transcriptc.561A>G p.Val187= synonymous_variant 4/131 NM_020853.2 P1
FAM234BENST00000416494.6 linkuse as main transcriptc.561A>G p.Val187= synonymous_variant, NMD_transcript_variant 4/142

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.728
AC:
110412
AN:
151636
Hom.:
41897
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.522
Gnomad AMI
AF:
0.701
Gnomad AMR
AF:
0.749
Gnomad ASJ
AF:
0.778
Gnomad EAS
AF:
0.473
Gnomad SAS
AF:
0.720
Gnomad FIN
AF:
0.779
Gnomad MID
AF:
0.785
Gnomad NFE
AF:
0.857
Gnomad OTH
AF:
0.748
GnomAD3 exomes
AF:
0.745
AC:
186428
AN:
250076
Hom.:
71801
AF XY:
0.757
AC XY:
102280
AN XY:
135084
show subpopulations
Gnomad AFR exome
AF:
0.510
Gnomad AMR exome
AF:
0.620
Gnomad ASJ exome
AF:
0.767
Gnomad EAS exome
AF:
0.470
Gnomad SAS exome
AF:
0.726
Gnomad FIN exome
AF:
0.787
Gnomad NFE exome
AF:
0.856
Gnomad OTH exome
AF:
0.784
GnomAD4 exome
AF:
0.823
AC:
1201736
AN:
1460920
Hom.:
500694
Cov.:
43
AF XY:
0.821
AC XY:
596812
AN XY:
726698
show subpopulations
Gnomad4 AFR exome
AF:
0.513
Gnomad4 AMR exome
AF:
0.637
Gnomad4 ASJ exome
AF:
0.763
Gnomad4 EAS exome
AF:
0.509
Gnomad4 SAS exome
AF:
0.730
Gnomad4 FIN exome
AF:
0.791
Gnomad4 NFE exome
AF:
0.862
Gnomad4 OTH exome
AF:
0.797
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.728
AC:
110429
AN:
151754
Hom.:
41896
Cov.:
31
AF XY:
0.723
AC XY:
53620
AN XY:
74144
show subpopulations
Gnomad4 AFR
AF:
0.521
Gnomad4 AMR
AF:
0.748
Gnomad4 ASJ
AF:
0.778
Gnomad4 EAS
AF:
0.472
Gnomad4 SAS
AF:
0.721
Gnomad4 FIN
AF:
0.779
Gnomad4 NFE
AF:
0.857
Gnomad4 OTH
AF:
0.748
Alfa
AF:
0.817
Hom.:
64205
Bravo
AF:
0.709
Asia WGS
AF:
0.569
AC:
1982
AN:
3478
EpiCase
AF:
0.854
EpiControl
AF:
0.852

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

FAM234B-related disorder Benign:1
Benign, criteria provided, single submitterclinical testingPreventionGenetics, part of Exact SciencesOct 16, 2019This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.55
Cadd
Benign
8.4
Dann
Benign
0.76

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs3741818; hg19: chr12-13214537; COSMIC: COSV52195016; COSMIC: COSV52195016; API