2-188595826-T-C
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1
The NM_016315.4(GULP1):c.*1815T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.81 in 152,070 control chromosomes in the GnomAD database, including 51,194 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 0.81 ( 51022 hom., cov: 32)
Exomes 𝑓: 0.89 ( 172 hom. )
Consequence
GULP1
NM_016315.4 3_prime_UTR
NM_016315.4 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.274
Genes affected
GULP1 (HGNC:18649): (GULP PTB domain containing engulfment adaptor 1) The protein encoded by this gene is an adapter protein necessary for the engulfment of apoptotic cells by phagocytes. Several transcript variants, some protein coding and some thought not to be protein coding, have been found for this gene. [provided by RefSeq, Nov 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.34).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.945 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GULP1 | ENST00000409830.6 | c.*1815T>C | 3_prime_UTR_variant | 12/12 | 1 | NM_016315.4 | ENSP00000386732.1 | |||
GULP1 | ENST00000359135.7 | c.*1815T>C | 3_prime_UTR_variant | 12/12 | 1 | ENSP00000352047.3 | ||||
GULP1 | ENST00000699998.1 | c.*1815T>C | 3_prime_UTR_variant | 13/13 | ENSP00000514748.1 | |||||
GULP1 | ENST00000409580.5 | c.*1815T>C | 3_prime_UTR_variant | 13/13 | 2 | ENSP00000386289.1 |
Frequencies
GnomAD3 genomes AF: 0.810 AC: 122674AN: 151522Hom.: 51012 Cov.: 32
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GnomAD4 exome AF: 0.887 AC: 383AN: 432Hom.: 172 Cov.: 0 AF XY: 0.888 AC XY: 231AN XY: 260
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GnomAD4 genome AF: 0.809 AC: 122722AN: 151638Hom.: 51022 Cov.: 32 AF XY: 0.813 AC XY: 60230AN XY: 74108
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ClinVar
Not reported inComputational scores
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at