2-119453277-G-A
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_002980.3(SCTR):c.851+10C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00472 in 1,596,678 control chromosomes in the GnomAD database, including 239 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.022 ( 132 hom., cov: 33)
Exomes 𝑓: 0.0029 ( 107 hom. )
Consequence
SCTR
NM_002980.3 intron
NM_002980.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.267
Genes affected
SCTR (HGNC:10608): (secretin receptor) The protein encoded by this gene is a G protein-coupled receptor and belongs to the glucagon-VIP-secretin receptor family. It binds secretin which is the most potent regulator of pancreatic bicarbonate, electrolyte and volume secretion. Secretin and its receptor are suggested to be involved in pancreatic cancer and autism. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BP6
?
Variant 2-119453277-G-A is Benign according to our data. Variant chr2-119453277-G-A is described in ClinVar as [Benign]. Clinvar id is 780356.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0701 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SCTR | NM_002980.3 | c.851+10C>T | intron_variant | ENST00000019103.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SCTR | ENST00000019103.8 | c.851+10C>T | intron_variant | 1 | NM_002980.3 | P1 | |||
SCTR | ENST00000485440.1 | n.1531+10C>T | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0218 AC: 3313AN: 152152Hom.: 132 Cov.: 33
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GnomAD3 exomes AF: 0.00652 AC: 1639AN: 251350Hom.: 49 AF XY: 0.00498 AC XY: 677AN XY: 135870
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GnomAD4 exome AF: 0.00292 AC: 4212AN: 1444408Hom.: 107 Cov.: 28 AF XY: 0.00265 AC XY: 1909AN XY: 719770
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GnomAD4 genome ? AF: 0.0218 AC: 3322AN: 152270Hom.: 132 Cov.: 33 AF XY: 0.0216 AC XY: 1612AN XY: 74460
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Aug 15, 2017 | - - |
Computational scores
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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