7-892317-C-T
Variant names:
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_ModerateBP6_ModerateBP7BS1BS2
The NM_015949.3(GET4):c.645C>T(p.Val215Val) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00105 in 1,594,456 control chromosomes in the GnomAD database, including 24 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0019 ( 2 hom., cov: 33)
Exomes 𝑓: 0.00096 ( 22 hom. )
Consequence
GET4
NM_015949.3 synonymous
NM_015949.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.483
Genes affected
GET4 (HGNC:21690): (guided entry of tail-anchored proteins factor 4) Enables chaperone binding activity. Involved in cytoplasmic sequestering of protein; maintenance of unfolded protein involved in ERAD pathway; and tail-anchored membrane protein insertion into ER membrane. Located in chromosome; cytosol; and nuclear lumen. Part of BAT3 complex. [provided by Alliance of Genome Resources, Apr 2022]
SUN1 (HGNC:18587): (Sad1 and UNC84 domain containing 1) This gene is a member of the unc-84 homolog family and encodes a nuclear envelope protein with an Unc84 (SUN) domain. The protein is involved in nuclear anchorage and migration. Alternatively spliced transcript variants have been described. [provided by RefSeq, Jan 2019]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.43).
BP6
Variant 7-892317-C-T is Benign according to our data. Variant chr7-892317-C-T is described in ClinVar as [Benign]. Clinvar id is 785870.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.483 with no splicing effect.
BS1
Variant frequency is greater than expected in population amr. gnomad4 allele frequency = 0.00185 (282/152340) while in subpopulation AMR AF= 0.0176 (270/15300). AF 95% confidence interval is 0.0159. There are 2 homozygotes in gnomad4. There are 172 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 2 AR gene
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00186 AC: 283AN: 152222Hom.: 2 Cov.: 33
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GnomAD3 exomes AF: 0.00456 AC: 1146AN: 251190Hom.: 20 AF XY: 0.00347 AC XY: 471AN XY: 135864
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GnomAD4 exome AF: 0.000963 AC: 1389AN: 1442116Hom.: 22 Cov.: 31 AF XY: 0.000819 AC XY: 584AN XY: 712636
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GnomAD4 genome AF: 0.00185 AC: 282AN: 152340Hom.: 2 Cov.: 33 AF XY: 0.00231 AC XY: 172AN XY: 74508
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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
May 15, 2018
Labcorp Genetics (formerly Invitae), Labcorp
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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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