chr10-113879701-T-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_198514.4(NHLRC2):c.909+6T>A variant causes a splice donor region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0139 in 1,448,580 control chromosomes in the GnomAD database, including 202 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.012 ( 18 hom., cov: 32)
Exomes 𝑓: 0.014 ( 184 hom. )
Consequence
NHLRC2
NM_198514.4 splice_donor_region, intron
NM_198514.4 splice_donor_region, intron
Scores
2
Splicing: ADA: 0.01105
2
Clinical Significance
Conservation
PhyloP100: 0.684
Genes affected
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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=-0.68).
BP6
?
Variant 10-113879701-T-A is Benign according to our data. Variant chr10-113879701-T-A is described in ClinVar as [Benign]. Clinvar id is 3041791.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.012 (1833/152156) while in subpopulation NFE AF= 0.0157 (1064/67960). AF 95% confidence interval is 0.0149. There are 18 homozygotes in gnomad4. There are 963 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 18 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NHLRC2 | NM_198514.4 | c.909+6T>A | splice_donor_region_variant, intron_variant | ENST00000369301.3 | |||
NHLRC2 | XM_011539769.4 | c.909+6T>A | splice_donor_region_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NHLRC2 | ENST00000369301.3 | c.909+6T>A | splice_donor_region_variant, intron_variant | 2 | NM_198514.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0120 AC: 1831AN: 152038Hom.: 18 Cov.: 32
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GnomAD3 exomes AF: 0.0155 AC: 2988AN: 192502Hom.: 52 AF XY: 0.0154 AC XY: 1635AN XY: 106190
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GnomAD4 exome AF: 0.0141 AC: 18290AN: 1296424Hom.: 184 Cov.: 21 AF XY: 0.0138 AC XY: 8984AN XY: 650024
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
NHLRC2-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | May 16, 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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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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dbscSNV1_ADA
Benign
dbscSNV1_RF
Benign
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at