chr6-41350840-T-C
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_004828.4(NCR2):c.807T>C(p.Asp269=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00444 in 885,666 control chromosomes in the GnomAD database, including 36 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0097 ( 18 hom., cov: 33)
Exomes 𝑓: 0.0034 ( 18 hom. )
Consequence
NCR2
NM_004828.4 synonymous
NM_004828.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.214
Genes affected
NCR2 (HGNC:6732): (natural cytotoxicity triggering receptor 2) Predicted to enable signaling receptor activity. Predicted to be involved in cellular defense response and signal transduction. Predicted to be located in plasma membrane. Predicted to be integral component of plasma membrane. Predicted to be active in cell surface. [provided by Alliance of Genome Resources, Apr 2022]
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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=-0.96).
BP6
?
Variant 6-41350840-T-C is Benign according to our data. Variant chr6-41350840-T-C is described in ClinVar as [Benign]. Clinvar id is 778229.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=0.214 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00969 (1476/152328) while in subpopulation AFR AF= 0.0251 (1044/41582). AF 95% confidence interval is 0.0238. There are 18 homozygotes in gnomad4. There are 707 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 17 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NCR2 | NM_004828.4 | c.807T>C | p.Asp269= | synonymous_variant | 5/5 | ENST00000373089.10 | |
NCR2 | NM_001199509.2 | c.*137T>C | 3_prime_UTR_variant | 6/6 | |||
NCR2 | NM_001199510.2 | c.*137T>C | 3_prime_UTR_variant | 6/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NCR2 | ENST00000373089.10 | c.807T>C | p.Asp269= | synonymous_variant | 5/5 | 1 | NM_004828.4 | P2 | |
NCR2 | ENST00000373083.8 | c.*137T>C | 3_prime_UTR_variant | 6/6 | 1 | A2 | |||
NCR2 | ENST00000373086.3 | c.*137T>C | 3_prime_UTR_variant | 6/6 | 1 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.00967 AC: 1472AN: 152210Hom.: 17 Cov.: 33
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GnomAD3 exomes AF: 0.00452 AC: 1043AN: 230778Hom.: 15 AF XY: 0.00411 AC XY: 513AN XY: 124956
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GnomAD4 exome AF: 0.00335 AC: 2458AN: 733338Hom.: 18 Cov.: 10 AF XY: 0.00310 AC XY: 1214AN XY: 391970
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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 | Jun 13, 2018 | - - |
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