rs3828357
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NR_024251.1(FAM86JP):n.1530T>C variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.358 in 1,596,110 control chromosomes in the GnomAD database, including 104,343 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.33 ( 8870 hom., cov: 32)
Exomes 𝑓: 0.36 ( 95473 hom. )
Consequence
FAM86JP
NR_024251.1 non_coding_transcript_exon
NR_024251.1 non_coding_transcript_exon
Scores
3
10
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 4.93
Genes affected
FAM86JP (HGNC:44097): (family with sequence similarity 86 member J, pseudogene)
ALG1L1P (HGNC:33721): (ALG1 like 1, pseudogene) Predicted to enable mannosyltransferase activity. Predicted to be involved in protein glycosylation. Predicted to be active in endoplasmic reticulum. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.013293445).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.374 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FAM86JP | NR_024251.1 | n.1530T>C | non_coding_transcript_exon_variant | 5/5 | |||
ALG1L1P | NR_171197.1 | n.481A>G | non_coding_transcript_exon_variant | 5/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ALG1L1P | ENST00000611639.4 | n.652A>G | non_coding_transcript_exon_variant | 7/7 | 3 | ||||
ENST00000692801.1 | n.580A>G | non_coding_transcript_exon_variant | 6/6 | ||||||
FAM86JP | ENST00000693415.1 | n.1274T>C | non_coding_transcript_exon_variant | 4/4 |
Frequencies
GnomAD3 genomes ? AF: 0.335 AC: 50864AN: 151892Hom.: 8873 Cov.: 32
GnomAD3 genomes
?
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GnomAD3 exomes AF: 0.336 AC: 78478AN: 233450Hom.: 13891 AF XY: 0.341 AC XY: 43764AN XY: 128302
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GnomAD4 exome AF: 0.360 AC: 520248AN: 1444100Hom.: 95473 Cov.: 73 AF XY: 0.360 AC XY: 258706AN XY: 718794
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GnomAD4 genome ? AF: 0.335 AC: 50862AN: 152010Hom.: 8870 Cov.: 32 AF XY: 0.333 AC XY: 24723AN XY: 74276
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T;T
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationTaster
Benign
P
PrimateAI
Uncertain
T
Sift4G
Uncertain
T;T
Polyphen
0.59
.;P
Vest4
MPC
0.0062
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at