6-118980271-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_024581.6(FAM184A):c.2168C>T(p.Thr723Met) variant causes a missense change. The variant allele was found at a frequency of 0.0000204 in 1,614,004 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000013 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000021 ( 0 hom. )
Consequence
FAM184A
NM_024581.6 missense
NM_024581.6 missense
Scores
2
4
8
Clinical Significance
Conservation
PhyloP100: 3.58
Genes affected
FAM184A (HGNC:20991): (family with sequence similarity 184 member A) Located in extracellular space. [provided by Alliance of Genome Resources, Apr 2022]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (MetaRNN=0.2365717).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FAM184A | NM_024581.6 | c.2168C>T | p.Thr723Met | missense_variant | 10/18 | ENST00000338891.12 | |
LOC124901389 | XR_007059729.1 | n.76+45281G>A | intron_variant, non_coding_transcript_variant | ||||
FAM184A | NM_001100411.3 | c.1808C>T | p.Thr603Met | missense_variant | 10/17 | ||
FAM184A | NM_001288576.2 | c.1808C>T | p.Thr603Met | missense_variant | 10/16 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FAM184A | ENST00000338891.12 | c.2168C>T | p.Thr723Met | missense_variant | 10/18 | 1 | NM_024581.6 | P1 | |
ENST00000518570.2 | n.222-26212G>A | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000132 AC: 2AN: 152070Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000201 AC: 5AN: 249360Hom.: 0 AF XY: 0.0000370 AC XY: 5AN XY: 135276
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GnomAD4 exome AF: 0.0000212 AC: 31AN: 1461816Hom.: 0 Cov.: 31 AF XY: 0.0000261 AC XY: 19AN XY: 727218
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GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152188Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74400
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 06, 2023 | The c.2168C>T (p.T723M) alteration is located in exon 10 (coding exon 10) of the FAM184A gene. This alteration results from a C to T substitution at nucleotide position 2168, causing the threonine (T) at amino acid position 723 to be replaced by a methionine (M). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Pathogenic
Dann
Pathogenic
DEOGEN2
Benign
T;T;.;T;.
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Pathogenic
D;D;D;D;D
M_CAP
Benign
T
MetaRNN
Benign
T;T;T;T;T
MetaSVM
Benign
T
MutationTaster
Benign
D;D;D;D
PrimateAI
Uncertain
T
Sift4G
Benign
T;D;T;T;D
Polyphen
1.0
.;D;.;.;D
Vest4
MVP
MPC
0.58
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at