12-103856016-T-C
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NR_027249.1(TTC41P):n.3706+1094A>G 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 0.951 in 152,332 control chromosomes in the GnomAD database, including 69,020 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 0.95 ( 69020 hom., cov: 33)
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: -0.482
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=-0.91).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TTC41P | NR_027249.1 | n.3706+1094A>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ENST00000548520.2 | n.2665+1094A>G | intron_variant, non_coding_transcript_variant | 5 | ||||||
TTC41P | ENST00000551270.1 | n.3160+1094A>G | intron_variant, non_coding_transcript_variant | ||||||
ENST00000548527.5 | n.804+1094A>G | intron_variant, non_coding_transcript_variant | 5 | ||||||
ENST00000552065.2 | n.2249+1094A>G | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.951 AC: 144817AN: 152214Hom.: 68963 Cov.: 33
GnomAD3 genomes
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144817
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152214
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33
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.951 AC: 144934AN: 152332Hom.: 69020 Cov.: 33 AF XY: 0.954 AC XY: 71036AN XY: 74486
GnomAD4 genome
?
AF:
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144934
AN:
152332
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Cov.:
33
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71036
AN XY:
74486
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Asia WGS
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3449
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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