16-13919809-A-C
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The XR_007065001.1(LOC124903647):n.270T>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.275 in 152,088 control chromosomes in the GnomAD database, including 5,831 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.27 ( 5831 hom., cov: 33)
Consequence
LOC124903647
XR_007065001.1 non_coding_transcript_exon
XR_007065001.1 non_coding_transcript_exon
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.92
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=-0.84).
BP6
Variant 16-13919809-A-C is Benign according to our data. Variant chr16-13919809-A-C is described in ClinVar as [Benign]. Clinvar id is 1164457.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.281 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LOC124903647 | XR_007065001.1 | n.270T>G | non_coding_transcript_exon_variant | 1/2 | |||
LOC105371093 | XR_007065000.1 | n.82+6716T>G | intron_variant, non_coding_transcript_variant | ||||
LOC105371093 | XR_007064999.1 | n.82+6716T>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
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Frequencies
GnomAD3 genomes AF: 0.274 AC: 41703AN: 151970Hom.: 5821 Cov.: 33
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.275 AC: 41759AN: 152088Hom.: 5831 Cov.: 33 AF XY: 0.272 AC XY: 20239AN XY: 74338
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Cockayne syndrome;C0268140:Xeroderma pigmentosum, group F;C3808988:Fanconi anemia complementation group Q Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jul 17, 2023 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at