rs10505599
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001382403.1(TMEM71):c.488-2745T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.11 in 152,194 control chromosomes in the GnomAD database, including 1,260 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 0.11 ( 1260 hom., cov: 32)
Consequence
TMEM71
NM_001382403.1 intron
NM_001382403.1 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.121
Genes affected
Genome browser will be placed here
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 (NFE) allele frequency at 95% confidence interval = 0.168 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TMEM71 | NM_001382403.1 | c.488-2745T>A | intron_variant | ENST00000677595.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TMEM71 | ENST00000677595.1 | c.488-2745T>A | intron_variant | NM_001382403.1 | P1 | ||||
TMEM71 | ENST00000356838.7 | c.431-2745T>A | intron_variant | 1 | |||||
TMEM71 | ENST00000377901.8 | c.488-8616T>A | intron_variant | 1 | |||||
TMEM71 | ENST00000523829.5 | c.488-2745T>A | intron_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.110 AC: 16708AN: 152076Hom.: 1260 Cov.: 32
GnomAD3 genomes
?
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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: 0.110 AC: 16706AN: 152194Hom.: 1260 Cov.: 32 AF XY: 0.108 AC XY: 8020AN XY: 74412
GnomAD4 genome
?
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AC:
16706
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152194
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32
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8020
AN XY:
74412
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65
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at