chr1-109194441-C-T
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_ModerateBP7BA1
The NM_020775.5(ELAPOR1):c.1968C>T(p.Asn656Asn) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.762 in 1,611,524 control chromosomes in the GnomAD database, including 476,407 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 0.67 ( 36892 hom., cov: 33)
Exomes 𝑓: 0.77 ( 439515 hom. )
Consequence
ELAPOR1
NM_020775.5 synonymous
NM_020775.5 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.19
Genes affected
ELAPOR1 (HGNC:29618): (endosome-lysosome associated apoptosis and autophagy regulator 1) Expression of this gene is induced by estrogen and the encoded protein has been characterized as a transmembrane protein. The encoded protein has been found in to correlate with survival in certain carcinomas (PMID: 21102415) and may be important for cellular response to stress (PMID: 21072319). Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2012]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.41).
BP7
Synonymous conserved (PhyloP=-2.18 with no splicing effect.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.95 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.669 AC: 101776AN: 152042Hom.: 36875 Cov.: 33
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GnomAD3 exomes AF: 0.784 AC: 197031AN: 251342Hom.: 79374 AF XY: 0.789 AC XY: 107206AN XY: 135842
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GnomAD4 exome AF: 0.771 AC: 1125432AN: 1459364Hom.: 439515 Cov.: 51 AF XY: 0.774 AC XY: 562389AN XY: 726144
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GnomAD4 genome AF: 0.669 AC: 101824AN: 152160Hom.: 36892 Cov.: 33 AF XY: 0.678 AC XY: 50446AN XY: 74404
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Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at