chr6-26383878-G-A
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BS1BS2
The NM_006995.5(BTN2A2):c.57G>A(p.Leu19=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0121 in 1,613,780 control chromosomes in the GnomAD database, including 159 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).
Frequency
Genomes: 𝑓 0.010 ( 13 hom., cov: 31)
Exomes 𝑓: 0.012 ( 146 hom. )
Consequence
BTN2A2
NM_006995.5 synonymous
NM_006995.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.145
Genes affected
BTN2A2 (HGNC:1137): (butyrophilin subfamily 2 member A2) Butyrophilin is the major protein associated with fat droplets in the milk. This gene is a member of the BTN2 subfamily of genes, which encode proteins belonging to the butyrophilin protein family. The gene is located in a cluster on chromosome 6, consisting of seven genes belonging to the expanding B7/butyrophilin-like group, a subset of the immunoglobulin gene superfamily. The encoded protein is a type I receptor glycoprotein involved in lipid, fatty-acid and sterol metabolism. Several alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2010]
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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 (BayesDel_noAF=-0.89).
BP6
Variant 6-26383878-G-A is Benign according to our data. Variant chr6-26383878-G-A is described in ClinVar as [Benign]. Clinvar id is 3057121.Status of the report is no_assertion_criteria_provided, 0 stars.
BP7
Synonymous conserved (PhyloP=-0.145 with no splicing effect.
BS1
Variant frequency is greater than expected in population amr. gnomad4 allele frequency = 0.0101 (1531/152120) while in subpopulation AMR AF= 0.0193 (294/15272). AF 95% confidence interval is 0.0174. There are 13 homozygotes in gnomad4. There are 734 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 13 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BTN2A2 | NM_006995.5 | c.57G>A | p.Leu19= | synonymous_variant | 2/8 | ENST00000356709.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BTN2A2 | ENST00000356709.9 | c.57G>A | p.Leu19= | synonymous_variant | 2/8 | 1 | NM_006995.5 | P1 | |
ENST00000707189.1 | n.1000-169309G>A | intron_variant, non_coding_transcript_variant | |||||||
ENST00000707191.1 | n.1001-148827G>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.0101 AC: 1533AN: 152002Hom.: 14 Cov.: 31
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GnomAD3 exomes AF: 0.0114 AC: 2848AN: 249958Hom.: 29 AF XY: 0.0122 AC XY: 1649AN XY: 135064
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GnomAD4 exome AF: 0.0123 AC: 18026AN: 1461660Hom.: 146 Cov.: 31 AF XY: 0.0126 AC XY: 9177AN XY: 727154
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GnomAD4 genome AF: 0.0101 AC: 1531AN: 152120Hom.: 13 Cov.: 31 AF XY: 0.00987 AC XY: 734AN XY: 74380
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
BTN2A2-related disorder Benign:1
Benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Apr 29, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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