rs7011101
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000262213.7(TRAM1):c.571-2063T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.122 in 152,226 control chromosomes in the GnomAD database, including 1,324 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 0.12 ( 1324 hom., cov: 32)
Consequence
TRAM1
ENST00000262213.7 intron
ENST00000262213.7 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 2.96
Genes affected
TRAM1 (HGNC:20568): (translocation associated membrane protein 1) This gene encodes a multi-pass membrane protein that is part of the mammalian endoplasmic reticulum. The encoded protein influences glycosylation and facilitates the translocation of secretory proteins across the endoplasmic reticulum membrane by regulating which domains of the nascent polypeptide chain are visible to the cytosol during a translocational pause. [provided by RefSeq, Oct 2009]
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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=-0.83).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.184 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TRAM1 | NM_014294.6 | c.571-2063T>G | intron_variant | ENST00000262213.7 | NP_055109.1 | |||
TRAM1 | NM_001317804.2 | c.478-2063T>G | intron_variant | NP_001304733.1 | ||||
TRAM1 | NM_001317805.2 | c.313-2063T>G | intron_variant | NP_001304734.1 | ||||
TRAM1 | XM_047421636.1 | c.313-2063T>G | intron_variant | XP_047277592.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TRAM1 | ENST00000262213.7 | c.571-2063T>G | intron_variant | 1 | NM_014294.6 | ENSP00000262213 | P1 | |||
TRAM1 | ENST00000521425.5 | c.313-2063T>G | intron_variant | 2 | ENSP00000428052 | |||||
TRAM1 | ENST00000521049.5 | n.445-1559T>G | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.122 AC: 18527AN: 152108Hom.: 1319 Cov.: 32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.122 AC: 18541AN: 152226Hom.: 1324 Cov.: 32 AF XY: 0.118 AC XY: 8760AN XY: 74440
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282
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3478
ClinVar
Not reported inComputational scores
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Name
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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