chr11-47587802-C-T

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_001164379.3(FAM180B):​c.137C>T​(p.Ala46Val) 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. 13/16 in silico tools predict a benign outcome for this variant. 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. A46D) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 32)

Consequence

FAM180B
NM_001164379.3 missense

Scores

1
16

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.98
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 Likely_benign. Variant got -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.050254643).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
FAM180BNM_001164379.3 linkc.137C>T p.Ala46Val missense_variant Exon 2 of 3 ENST00000538490.3 NP_001157851.1 Q6P0A1
FAM180BNM_001367968.1 linkc.-85C>T 5_prime_UTR_variant Exon 2 of 3 NP_001354897.1
FAM180BNM_001367966.1 linkc.86-202C>T intron_variant Intron 1 of 1 NP_001354895.1
FAM180BNM_001367967.1 linkc.7-237C>T intron_variant Intron 1 of 1 NP_001354896.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
FAM180BENST00000538490.3 linkc.137C>T p.Ala46Val missense_variant Exon 2 of 3 1 NM_001164379.3 ENSP00000443133.2 Q6P0A1

Frequencies

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

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.10
BayesDel_addAF
Benign
-0.32
T
BayesDel_noAF
Benign
-0.70
CADD
Benign
9.7
DANN
Uncertain
1.0
DEOGEN2
Benign
0.031
T
Eigen
Benign
-1.0
Eigen_PC
Benign
-0.92
FATHMM_MKL
Benign
0.056
N
M_CAP
Benign
0.0067
T
MetaRNN
Benign
0.050
T
MetaSVM
Benign
-1.0
T
PrimateAI
Benign
0.35
T
PROVEAN
Benign
-1.4
N
REVEL
Benign
0.042
Sift
Benign
0.34
T
Sift4G
Benign
0.14
T
Vest4
0.12
MVP
0.014
ClinPred
0.080
T
GERP RS
-1.6

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.090
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: chr11-47609354; API