17-46922868-C-T
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The XM_024450773.2(LRRC37A2):c.4810-126188C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00591 in 453,476 control chromosomes in the GnomAD database, including 56 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.014 ( 53 hom., cov: 32)
Exomes 𝑓: 0.0016 ( 3 hom. )
Consequence
LRRC37A2
XM_024450773.2 intron
XM_024450773.2 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.888
Genes affected
LRRC37A2 (HGNC:32404): (leucine rich repeat containing 37 member A2) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]
GOSR2-DT (HGNC:55346): (GOSR2 divergent transcript)
GOSR2 (HGNC:4431): (golgi SNAP receptor complex member 2) This gene encodes a trafficking membrane protein which transports proteins among the medial- and trans-Golgi compartments. Due to its chromosomal location and trafficking function, this gene may be involved in familial essential hypertension. [provided by RefSeq, Mar 2016]
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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=-0.75).
BP6
Variant 17-46922868-C-T is Benign according to our data. Variant chr17-46922868-C-T is described in ClinVar as [Benign]. Clinvar id is 1241591.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0144 (2187/152328) while in subpopulation AFR AF= 0.0503 (2090/41572). AF 95% confidence interval is 0.0485. There are 53 homozygotes in gnomad4. There are 1020 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 53 AR gene
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GOSR2-DT | ENST00000572349.1 | n.167G>A | non_coding_transcript_exon_variant | Exon 1 of 3 | 3 | |||||
GOSR2 | ENST00000640608.1 | c.-325C>T | upstream_gene_variant | 2 | ENSP00000491979.1 | |||||
GOSR2 | ENST00000638634.1 | c.-325C>T | upstream_gene_variant | 5 | ENSP00000491946.1 |
Frequencies
GnomAD3 genomes AF: 0.0142 AC: 2168AN: 152210Hom.: 52 Cov.: 32
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GnomAD4 exome AF: 0.00163 AC: 492AN: 301148Hom.: 3 Cov.: 0 AF XY: 0.00125 AC XY: 198AN XY: 157994
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GnomAD4 genome AF: 0.0144 AC: 2187AN: 152328Hom.: 53 Cov.: 32 AF XY: 0.0137 AC XY: 1020AN XY: 74484
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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
Jun 22, 2018
GeneDx
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
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Computational scores
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Name
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at