chr1-169708538-A-G
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_000655.5(SELL):c.351T>C(p.Gly117=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00241 in 1,613,418 control chromosomes in the GnomAD database, including 81 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.013 ( 35 hom., cov: 32)
Exomes 𝑓: 0.0013 ( 46 hom. )
Consequence
SELL
NM_000655.5 synonymous
NM_000655.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.08
Genes affected
SELL (HGNC:10720): (selectin L) This gene encodes a cell surface adhesion molecule that belongs to a family of adhesion/homing receptors. The encoded protein contains a C-type lectin-like domain, a calcium-binding epidermal growth factor-like domain, and two short complement-like repeats. The gene product is required for binding and subsequent rolling of leucocytes on endothelial cells, facilitating their migration into secondary lymphoid organs and inflammation sites. Single-nucleotide polymorphisms in this gene have been associated with various diseases including immunoglobulin A nephropathy. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Oct 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.78).
BP6
?
Variant 1-169708538-A-G is Benign according to our data. Variant chr1-169708538-A-G is described in ClinVar as [Benign]. Clinvar id is 789697.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-2.08 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0126 (1920/152160) while in subpopulation AFR AF= 0.0433 (1797/41510). AF 95% confidence interval is 0.0416. There are 35 homozygotes in gnomad4. There are 909 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 35 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SELL | NM_000655.5 | c.351T>C | p.Gly117= | synonymous_variant | 3/9 | ENST00000236147.6 | |
SELL | NR_029467.2 | n.320T>C | non_coding_transcript_exon_variant | 1/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SELL | ENST00000236147.6 | c.351T>C | p.Gly117= | synonymous_variant | 3/9 | 1 | NM_000655.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0125 AC: 1905AN: 152042Hom.: 35 Cov.: 32
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GnomAD3 exomes AF: 0.00314 AC: 781AN: 248502Hom.: 12 AF XY: 0.00234 AC XY: 316AN XY: 134810
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GnomAD4 exome AF: 0.00135 AC: 1970AN: 1461258Hom.: 46 Cov.: 31 AF XY: 0.00110 AC XY: 802AN XY: 726916
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GnomAD4 genome ? AF: 0.0126 AC: 1920AN: 152160Hom.: 35 Cov.: 32 AF XY: 0.0122 AC XY: 909AN XY: 74376
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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 31, 2019 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at