chr6-43516905-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_015388.4(YIPF3):c.-98C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0383 in 1,383,732 control chromosomes in the GnomAD database, including 1,456 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.054 ( 329 hom., cov: 33)
Exomes 𝑓: 0.036 ( 1127 hom. )
Consequence
YIPF3
NM_015388.4 5_prime_UTR
NM_015388.4 5_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0140
Genes affected
YIPF3 (HGNC:21023): (Yip1 domain family member 3) Predicted to be involved in cell differentiation. Located in Golgi apparatus and transport vesicle. [provided by Alliance of Genome Resources, Apr 2022]
POLR1C (HGNC:20194): (RNA polymerase I and III subunit C) The protein encoded by this gene is a subunit of both RNA polymerase I and RNA polymerase III complexes. The encoded protein is part of the Pol core element. Mutations in this gene have been associated with Treacher Collins syndrome (TCS) and hypomyelinating leukodystrophy 11. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 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=-0.73).
BP6
?
Variant 6-43516905-G-A is Benign according to our data. Variant chr6-43516905-G-A is described in ClinVar as [Benign]. Clinvar id is 1281294.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.105 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
YIPF3 | NM_015388.4 | c.-98C>T | 5_prime_UTR_variant | 1/9 | ENST00000372422.7 | ||
YIPF3 | XM_047418608.1 | c.-529C>T | 5_prime_UTR_variant | 1/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
YIPF3 | ENST00000372422.7 | c.-98C>T | 5_prime_UTR_variant | 1/9 | 1 | NM_015388.4 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.0544 AC: 8276AN: 152232Hom.: 328 Cov.: 33
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GnomAD4 exome AF: 0.0363 AC: 44726AN: 1231382Hom.: 1127 Cov.: 17 AF XY: 0.0376 AC XY: 23078AN XY: 614452
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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 | GeneDx | Jul 09, 2018 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at