6-118980242-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_024581.6(FAM184A):c.2197C>A(p.Leu733Ile) variant causes a missense change. The variant allele was found at a frequency of 0.0000204 in 1,613,918 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
4
10
Clinical Significance
Conservation
PhyloP100: 5.06
Genes affected
FAM184A (HGNC:20991): (family with sequence similarity 184 member A) Located in extracellular space. [provided by Alliance of Genome Resources, Apr 2022]
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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=0.1510039).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FAM184A | NM_024581.6 | c.2197C>A | p.Leu733Ile | missense_variant | 10/18 | ENST00000338891.12 | |
LOC124901389 | XR_007059729.1 | n.76+45252G>T | intron_variant, non_coding_transcript_variant | ||||
FAM184A | NM_001100411.3 | c.1837C>A | p.Leu613Ile | missense_variant | 10/17 | ||
FAM184A | NM_001288576.2 | c.1837C>A | p.Leu613Ile | missense_variant | 10/16 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FAM184A | ENST00000338891.12 | c.2197C>A | p.Leu733Ile | missense_variant | 10/18 | 1 | NM_024581.6 | P1 | |
ENST00000518570.2 | n.222-26241G>T | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000132 AC: 2AN: 152080Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.00000401 AC: 1AN: 249414Hom.: 0 AF XY: 0.00000739 AC XY: 1AN XY: 135310
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GnomAD4 exome AF: 0.0000212 AC: 31AN: 1461838Hom.: 0 Cov.: 31 AF XY: 0.0000193 AC XY: 14AN XY: 727224
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GnomAD4 genome ? AF: 0.0000132 AC: 2AN: 152080Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74262
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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 | Apr 06, 2023 | The c.2197C>A (p.L733I) alteration is located in exon 10 (coding exon 10) of the FAM184A gene. This alteration results from a C to A substitution at nucleotide position 2197, causing the leucine (L) at amino acid position 733 to be replaced by an isoleucine (I). 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
Benign
Dann
Uncertain
DEOGEN2
Benign
T;T;.;T;.
Eigen
Benign
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T;T;T;T;T
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;T;T;T;T
Polyphen
0.12, 0.096
.;B;.;.;B
Vest4
MVP
MPC
0.65
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