12-57621734-C-T
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Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_ModerateBP6_Moderate
The NR_120450.1(LOC101927583):n.170G>A 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 0.000000686 in 1,457,538 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 6.9e-7 ( 0 hom. )
Consequence
LOC101927583
NR_120450.1 non_coding_transcript_exon
NR_120450.1 non_coding_transcript_exon
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.38
Genes affected
SLC26A10P (HGNC:14470): (solute carrier family 26 member 10, pseudogene) Predicted to enable anion transmembrane transporter activity. Predicted to be involved in anion transport. Predicted to be active in basolateral plasma membrane. Predicted to be integral component of plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.46).
BP6
Variant 12-57621734-C-T is Benign according to our data. Variant chr12-57621734-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 739825.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LOC101927583 | NR_120450.1 | n.170G>A | non_coding_transcript_exon_variant | 1/4 | |||
SLC26A10P | NR_166679.1 | n.1294C>T | non_coding_transcript_exon_variant | 4/16 | |||
SLC26A10P | NR_166678.1 | n.1294C>T | non_coding_transcript_exon_variant | 4/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ENST00000440686.5 | n.472C>T | non_coding_transcript_exon_variant | 4/16 | 2 | |||||
SLC26A10P | ENST00000665594.1 | n.831C>T | non_coding_transcript_exon_variant | 5/18 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
GnomAD4 exome AF: 6.86e-7 AC: 1AN: 1457538Hom.: 0 Cov.: 33 AF XY: 0.00000138 AC XY: 1AN XY: 724608
GnomAD4 exome
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1
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1457538
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33
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1
AN XY:
724608
Gnomad4 AFR exome
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GnomAD4 genome Cov.: 32
GnomAD4 genome
Cov.:
32
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Apr 10, 2018 | - - |
Computational scores
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Name
Calibrated prediction
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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