1-168581191-A-T
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_002995.3(XCL1):c.316A>T(p.Thr106Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0013 in 1,613,642 control chromosomes in the GnomAD database, including 36 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0070 ( 17 hom., cov: 32)
Exomes 𝑓: 0.00071 ( 19 hom. )
Consequence
XCL1
NM_002995.3 missense
NM_002995.3 missense
Scores
18
Clinical Significance
Conservation
PhyloP100: 1.61
Genes affected
XCL1 (HGNC:10645): (X-C motif chemokine ligand 1) This antimicrobial gene encodes a member of the chemokine superfamily. Chemokines function in inflammatory and immunological responses, inducing leukocyte migration and activation. The encoded protein is a member of the C-chemokine subfamily, retaining only two of four cysteines conserved in other chemokines, and is thought to be specifically chemotactic for T cells. This gene and a closely related family member are located on the long arm of chromosome 1. [provided by RefSeq, Sep 2014]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.0035821497).
BP6
?
Variant 1-168581191-A-T is Benign according to our data. Variant chr1-168581191-A-T is described in ClinVar as [Benign]. Clinvar id is 780276.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00699 (1064/152132) while in subpopulation AFR AF= 0.0242 (1005/41458). AF 95% confidence interval is 0.023. There are 17 homozygotes in gnomad4. There are 531 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd4 at 17 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
XCL1 | NM_002995.3 | c.316A>T | p.Thr106Ser | missense_variant | 3/3 | ENST00000367818.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
XCL1 | ENST00000367818.4 | c.316A>T | p.Thr106Ser | missense_variant | 3/3 | 1 | NM_002995.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00699 AC: 1063AN: 152014Hom.: 17 Cov.: 32
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GnomAD3 exomes AF: 0.00171 AC: 430AN: 250934Hom.: 7 AF XY: 0.00129 AC XY: 175AN XY: 135620
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GnomAD4 exome AF: 0.000707 AC: 1033AN: 1461510Hom.: 19 Cov.: 30 AF XY: 0.000615 AC XY: 447AN XY: 727072
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GnomAD4 genome ? AF: 0.00699 AC: 1064AN: 152132Hom.: 17 Cov.: 32 AF XY: 0.00714 AC XY: 531AN XY: 74362
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 04, 2017 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
DEOGEN2
Benign
T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Benign
L
MutationTaster
Benign
N
PrimateAI
Benign
T
PROVEAN
Benign
N
REVEL
Benign
Sift
Benign
D
Sift4G
Benign
T
Polyphen
B
Vest4
MutPred
Gain of sheet (P = 0.0344);
MVP
MPC
ClinPred
T
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Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at