chr11-47586799-C-G

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_001164379.3(FAM180B):​c.31C>G​(p.Leu11Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 14/16 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 32)

Consequence

FAM180B
NM_001164379.3 missense

Scores

17

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: -0.0170
Variant links:
Genes affected
FAM180B (HGNC:34451): (family with sequence similarity 180 member B) Predicted to be located in extracellular region. [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=0.09335348).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
FAM180BNM_001164379.3 linkc.31C>G p.Leu11Val missense_variant Exon 1 of 3 ENST00000538490.3 NP_001157851.1 Q6P0A1
FAM180BNM_001367966.1 linkc.31C>G p.Leu11Val missense_variant Exon 1 of 2 NP_001354895.1
FAM180BNM_001367967.1 linkc.-49C>G 5_prime_UTR_variant Exon 1 of 2 NP_001354896.1
FAM180BNM_001367968.1 linkc.-191C>G 5_prime_UTR_variant Exon 1 of 3 NP_001354897.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
FAM180BENST00000538490.3 linkc.31C>G p.Leu11Val missense_variant Exon 1 of 3 1 NM_001164379.3 ENSP00000443133.2 Q6P0A1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
31
GnomAD4 genome
Cov.:
32

ClinVar

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

Submissions by phenotype

not specified Uncertain:1
Jan 27, 2025
Ambry Genetics
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The c.31C>G (p.L11V) alteration is located in exon 1 (coding exon 1) of the FAM180B gene. This alteration results from a C to G substitution at nucleotide position 31, causing the leucine (L) at amino acid position 11 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.080
BayesDel_addAF
Benign
-0.24
T
BayesDel_noAF
Benign
-0.59
CADD
Benign
13
DANN
Benign
0.84
DEOGEN2
Benign
0.030
T
Eigen
Benign
-0.78
Eigen_PC
Benign
-0.84
FATHMM_MKL
Benign
0.058
N
M_CAP
Benign
0.0063
T
MetaRNN
Benign
0.093
T
MetaSVM
Benign
-1.1
T
PrimateAI
Benign
0.32
T
PROVEAN
Benign
-1.2
N
REVEL
Benign
0.033
Sift
Benign
0.037
D
Sift4G
Benign
0.12
T
Vest4
0.30
MVP
0.014
ClinPred
0.16
T
GERP RS
2.4

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr11-47608351; API