rs11111839
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NR_027249.1(TTC41P):n.331-862G>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.08 in 152,180 control chromosomes in the GnomAD database, including 642 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.080 ( 642 hom., cov: 32)
Consequence
TTC41P
NR_027249.1 intron, non_coding_transcript
NR_027249.1 intron, non_coding_transcript
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.623
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.78).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.173 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TTC41P | NR_027249.1 | n.331-862G>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ENST00000388789.4 | n.251-862G>T | intron_variant, non_coding_transcript_variant | 1 | ||||||
ENST00000548520.2 | n.231-862G>T | intron_variant, non_coding_transcript_variant | 5 | ||||||
ENST00000548897.1 | n.942-862G>T | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0800 AC: 12163AN: 152062Hom.: 638 Cov.: 32
GnomAD3 genomes
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152062
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.0800 AC: 12179AN: 152180Hom.: 642 Cov.: 32 AF XY: 0.0807 AC XY: 6004AN XY: 74412
GnomAD4 genome
?
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12179
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152180
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32
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6004
AN XY:
74412
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Asia WGS
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522
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3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at