chr19-49970473-G-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The ENST00000602139.6(SIGLEC16):c.571G>A(p.Asp191Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 4/4 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0014 ( 1 hom., cov: 24)
Exomes 𝑓: 0.0014 ( 13 hom. )
Failed GnomAD Quality Control
Consequence
SIGLEC16
ENST00000602139.6 missense
ENST00000602139.6 missense
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.21
Genes affected
SIGLEC16 (HGNC:24851): (sialic acid binding Ig like lectin 16) Predicted to enable sialic acid binding activity. Involved in positive regulation of defense response to bacterium and positive regulation of interleukin-6 production. Predicted to be integral component of membrane. Predicted to be active in plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-1.02).
BP6
?
Variant 19-49970473-G-A is Benign according to our data. Variant chr19-49970473-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2650295.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
?
High Homozygotes in GnomAdExome at 6 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SIGLEC16 | NR_145574.2 | n.609G>A | non_coding_transcript_exon_variant | 3/9 | |||
SIGLEC16 | NM_001348364.2 | c.569G>A | p.Arg190Lys | missense_variant | 4/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SIGLEC16 | ENST00000602139.6 | c.571G>A | p.Asp191Asn | missense_variant | 3/9 | 5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00142 AC: 196AN: 138068Hom.: 1 Cov.: 24
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GnomAD3 exomes AF: 0.00206 AC: 409AN: 198628Hom.: 6 AF XY: 0.00236 AC XY: 254AN XY: 107804
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00138 AC: 1918AN: 1394802Hom.: 13 Cov.: 31 AF XY: 0.00154 AC XY: 1068AN XY: 693324
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GnomAD4 genome ? Data not reliable, filtered out with message: AS_VQSR AF: 0.00140 AC: 194AN: 138184Hom.: 1 Cov.: 24 AF XY: 0.00160 AC XY: 107AN XY: 67034
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Mar 01, 2023 | SIGLEC16: BS2 - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at