2-119464135-G-A
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Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_002980.3(SCTR):c.624C>T(p.Cys208=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00408 in 1,614,134 control chromosomes in the GnomAD database, including 35 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0038 ( 4 hom., cov: 32)
Exomes 𝑓: 0.0041 ( 31 hom. )
Consequence
SCTR
NM_002980.3 synonymous
NM_002980.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.997
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 -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.8).
BP6
?
Variant 2-119464135-G-A is Benign according to our data. Variant chr2-119464135-G-A is described in ClinVar as [Benign]. Clinvar id is 710545.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-0.997 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population mid. gnomad4_exome allele frequency = 0.00411 (6014/1461808) while in subpopulation MID AF= 0.0265 (153/5766). AF 95% confidence interval is 0.0231. There are 31 homozygotes in gnomad4_exome. There are 3031 alleles in male gnomad4_exome subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd4 at 4 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SCTR | NM_002980.3 | c.624C>T | p.Cys208= | synonymous_variant | 6/13 | ENST00000019103.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SCTR | ENST00000019103.8 | c.624C>T | p.Cys208= | synonymous_variant | 6/13 | 1 | NM_002980.3 | P1 | |
SCTR | ENST00000627145.1 | c.699C>T | p.Cys233= | synonymous_variant | 7/8 | 5 | |||
SCTR | ENST00000630739.2 | c.420C>T | p.Cys140= | synonymous_variant | 7/8 | 5 | |||
SCTR | ENST00000485440.1 | n.1304C>T | non_coding_transcript_exon_variant | 3/10 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00378 AC: 576AN: 152208Hom.: 4 Cov.: 32
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GnomAD3 exomes AF: 0.00382 AC: 961AN: 251380Hom.: 3 AF XY: 0.00400 AC XY: 544AN XY: 135874
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GnomAD4 exome AF: 0.00411 AC: 6014AN: 1461808Hom.: 31 Cov.: 32 AF XY: 0.00417 AC XY: 3031AN XY: 727214
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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 | Jun 25, 2018 | - - |
Computational scores
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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