chr10-95755831-T-C
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NR_038444.1(ENTPD1-AS1):n.1637A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.042 in 1,511,276 control chromosomes in the GnomAD database, including 1,540 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.034 ( 119 hom., cov: 31)
Exomes 𝑓: 0.043 ( 1421 hom. )
Consequence
ENTPD1-AS1
NR_038444.1 non_coding_transcript_exon
NR_038444.1 non_coding_transcript_exon
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.192
Genes affected
ENTPD1 (HGNC:3363): (ectonucleoside triphosphate diphosphohydrolase 1) The protein encoded by this gene is a plasma membrane protein that hydrolyzes extracellular ATP and ADP to AMP. Inhibition of this protein's activity may confer anticancer benefits. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Aug 2015]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BP6
Variant 10-95755831-T-C is Benign according to our data. Variant chr10-95755831-T-C is described in ClinVar as [Benign]. Clinvar id is 1234750.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS1
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0338 (5131/151994) while in subpopulation NFE AF= 0.0494 (3356/67976). AF 95% confidence interval is 0.048. There are 119 homozygotes in gnomad4. There are 2470 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 119 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ENTPD1-AS1 | NR_038444.1 | n.1637A>G | non_coding_transcript_exon_variant | 6/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ENTPD1-AS1 | ENST00000669711.1 | n.882A>G | non_coding_transcript_exon_variant | 6/7 |
Frequencies
GnomAD3 genomes AF: 0.0338 AC: 5136AN: 151876Hom.: 119 Cov.: 31
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GnomAD4 exome AF: 0.0429 AC: 58335AN: 1359282Hom.: 1421 Cov.: 25 AF XY: 0.0424 AC XY: 28508AN XY: 672240
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GnomAD4 genome AF: 0.0338 AC: 5131AN: 151994Hom.: 119 Cov.: 31 AF XY: 0.0332 AC XY: 2470AN XY: 74288
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Apr 08, 2021 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at