chr16-261507-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_032039.4(FAM234A):c.701G>A(p.Arg234Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0017 in 1,602,882 control chromosomes in the GnomAD database, including 38 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0077 ( 16 hom., cov: 33)
Exomes 𝑓: 0.0011 ( 22 hom. )
Consequence
FAM234A
NM_032039.4 missense
NM_032039.4 missense
Scores
16
Clinical Significance
Conservation
PhyloP100: -0.154
Genes affected
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.0027927756).
BP6
?
Variant 16-261507-G-A is Benign according to our data. Variant chr16-261507-G-A is described in ClinVar as [Benign]. Clinvar id is 778576.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00771 (1175/152316) while in subpopulation AFR AF= 0.0257 (1068/41564). AF 95% confidence interval is 0.0244. There are 16 homozygotes in gnomad4. There are 546 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 15 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FAM234A | NM_032039.4 | c.701G>A | p.Arg234Gln | missense_variant | 6/13 | ENST00000399932.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FAM234A | ENST00000399932.8 | c.701G>A | p.Arg234Gln | missense_variant | 6/13 | 1 | NM_032039.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00764 AC: 1163AN: 152198Hom.: 15 Cov.: 33
GnomAD3 genomes
?
AF:
AC:
1163
AN:
152198
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:
GnomAD3 exomes AF: 0.00246 AC: 556AN: 226440Hom.: 7 AF XY: 0.00205 AC XY: 254AN XY: 123630
GnomAD3 exomes
AF:
AC:
556
AN:
226440
Hom.:
AF XY:
AC XY:
254
AN XY:
123630
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.00106 AC: 1544AN: 1450566Hom.: 22 Cov.: 30 AF XY: 0.00104 AC XY: 751AN XY: 721086
GnomAD4 exome
AF:
AC:
1544
AN:
1450566
Hom.:
Cov.:
30
AF XY:
AC XY:
751
AN XY:
721086
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.00771 AC: 1175AN: 152316Hom.: 16 Cov.: 33 AF XY: 0.00733 AC XY: 546AN XY: 74480
GnomAD4 genome
?
AF:
AC:
1175
AN:
152316
Hom.:
Cov.:
33
AF XY:
AC XY:
546
AN XY:
74480
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
TwinsUK
AF:
AC:
1
ALSPAC
AF:
AC:
2
ESP6500AA
AF:
AC:
81
ESP6500EA
AF:
AC:
1
ExAC
?
AF:
AC:
349
Asia WGS
AF:
AC:
16
AN:
3478
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | May 30, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
DEOGEN2
Benign
T;.;.;.;T;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
MetaRNN
Benign
T;T;T;T;T;T
MetaSVM
Benign
T
MutationTaster
Benign
N;N;N;N;N
PrimateAI
Benign
T
PROVEAN
Benign
N;N;N;N;N;.
REVEL
Benign
Sift
Benign
T;T;T;T;T;.
Sift4G
Benign
T;T;T;T;T;T
Polyphen
B;B;.;.;B;.
Vest4
MVP
MPC
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
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