11-18701612-C-T

Variant summary

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

The NM_153347.3(TMEM86A):​c.326C>T​(p.Ser109Leu) variant causes a missense change. The variant allele was found at a frequency of 0.0000014 in 1,429,878 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 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)
Exomes 𝑓: 0.0000014 ( 0 hom. )

Consequence

TMEM86A
NM_153347.3 missense

Scores

3
16

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 4.64
Variant links:
Genes affected
TMEM86A (HGNC:26890): (transmembrane protein 86A) Predicted to enable alkenylglycerophosphocholine hydrolase activity and alkenylglycerophosphoethanolamine hydrolase activity. Predicted to be integral component of membrane. [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=0.15996638).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
TMEM86ANM_153347.3 linkuse as main transcriptc.326C>T p.Ser109Leu missense_variant 3/3 ENST00000280734.3 NP_699178.1
TMEM86AXM_047426448.1 linkuse as main transcriptc.326C>T p.Ser109Leu missense_variant 3/4 XP_047282404.1
TMEM86AXM_047426449.1 linkuse as main transcriptc.326C>T p.Ser109Leu missense_variant 3/5 XP_047282405.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
TMEM86AENST00000280734.3 linkuse as main transcriptc.326C>T p.Ser109Leu missense_variant 3/31 NM_153347.3 ENSP00000280734 P1
TMEM86AENST00000527002.5 linkuse as main transcriptn.561C>T non_coding_transcript_exon_variant 3/34
TMEM86AENST00000529240.1 linkuse as main transcriptn.446C>T non_coding_transcript_exon_variant 3/34

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD3 exomes
AF:
0.00000434
AC:
1
AN:
230510
Hom.:
0
AF XY:
0.00000808
AC XY:
1
AN XY:
123786
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.0000312
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.00000140
AC:
2
AN:
1429878
Hom.:
0
Cov.:
31
AF XY:
0.00
AC XY:
0
AN XY:
707192
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000183
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
32
Bravo
AF:
0.00000378

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 submitterclinical testingAmbry GeneticsMar 19, 2024The c.326C>T (p.S109L) alteration is located in exon 3 (coding exon 3) of the TMEM86A gene. This alteration results from a C to T substitution at nucleotide position 326, causing the serine (S) at amino acid position 109 to be replaced by a leucine (L). 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
0.14
BayesDel_addAF
Benign
-0.12
T
BayesDel_noAF
Benign
-0.41
CADD
Benign
22
DANN
Benign
0.85
DEOGEN2
Benign
0.0076
T
Eigen
Benign
-0.27
Eigen_PC
Benign
-0.069
FATHMM_MKL
Uncertain
0.96
D
LIST_S2
Uncertain
0.86
D
M_CAP
Benign
0.0090
T
MetaRNN
Benign
0.16
T
MetaSVM
Benign
-1.1
T
MutationAssessor
Benign
0.91
L
MutationTaster
Benign
1.0
D;D
PrimateAI
Uncertain
0.69
T
PROVEAN
Benign
-0.50
N
REVEL
Benign
0.090
Sift
Benign
0.66
T
Sift4G
Benign
0.67
T
Polyphen
0.0080
B
Vest4
0.36
MutPred
0.44
Loss of glycosylation at S109 (P = 0.0163);
MVP
0.12
MPC
0.37
ClinPred
0.24
T
GERP RS
4.1
Varity_R
0.082
gMVP
0.61

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs980122968; hg19: chr11-18723159; API