chr1-231040145-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_198552.3(FAM89A):​c.67G>A​(p.Gly23Arg) variant causes a missense change. The variant allele was found at a frequency of 0.0000017 in 1,177,574 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G23W) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 31)
Exomes 𝑓: 0.0000017 ( 0 hom. )

Consequence

FAM89A
NM_198552.3 missense

Scores

4
7
8

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.63
Variant links:
Genes affected
FAM89A (HGNC:25057): (family with sequence similarity 89 member A)

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
FAM89ANM_198552.3 linkc.67G>A p.Gly23Arg missense_variant Exon 1 of 2 ENST00000366654.5 NP_940954.1 Q96GI7

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
FAM89AENST00000366654.5 linkc.67G>A p.Gly23Arg missense_variant Exon 1 of 2 1 NM_198552.3 ENSP00000355614.4 Q96GI7

Frequencies

GnomAD3 genomes
Cov.:
31
GnomAD3 exomes
AF:
0.0000156
AC:
1
AN:
64174
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
37658
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.0000866
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.00000170
AC:
2
AN:
1177574
Hom.:
0
Cov.:
31
AF XY:
0.00
AC XY:
0
AN XY:
574664
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.0000469
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000104
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.98
BayesDel_addAF
Uncertain
0.029
T
BayesDel_noAF
Benign
-0.20
CADD
Benign
22
DANN
Uncertain
1.0
DEOGEN2
Benign
0.20
T
Eigen
Benign
-0.0036
Eigen_PC
Benign
-0.0084
FATHMM_MKL
Uncertain
0.83
D
LIST_S2
Benign
0.83
T
M_CAP
Pathogenic
0.42
D
MetaRNN
Uncertain
0.51
D
MetaSVM
Benign
-0.82
T
MutationAssessor
Uncertain
2.6
M
PrimateAI
Pathogenic
0.93
D
PROVEAN
Uncertain
-4.3
D
REVEL
Benign
0.18
Sift
Uncertain
0.0010
D
Sift4G
Pathogenic
0.0
D
Polyphen
0.61
P
Vest4
0.69
MutPred
0.35
Gain of MoRF binding (P = 0.0187);
MVP
0.085
MPC
0.34
ClinPred
0.96
D
GERP RS
3.0
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7
Varity_R
0.53
gMVP
0.60

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
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: rs746989013; hg19: chr1-231175891; API