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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

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.997
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.8).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
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
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=-0.997 with no splicing effect.
BS1
?
    BS1 - Allele frequency is greater than expected for disorder
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
?
    BS2 - Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age
High Homozygotes in GnomAd4 at 4 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SCTRNM_002980.3 linkuse as main transcriptc.624C>T p.Cys208= synonymous_variant 6/13 ENST00000019103.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SCTRENST00000019103.8 linkuse as main transcriptc.624C>T p.Cys208= synonymous_variant 6/131 NM_002980.3 P1
SCTRENST00000627145.1 linkuse as main transcriptc.699C>T p.Cys233= synonymous_variant 7/85
SCTRENST00000630739.2 linkuse as main transcriptc.420C>T p.Cys140= synonymous_variant 7/85
SCTRENST00000485440.1 linkuse as main transcriptn.1304C>T non_coding_transcript_exon_variant 3/102

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00378
AC:
576
AN:
152208
Hom.:
4
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.000796
Gnomad AMI
AF:
0.0680
Gnomad AMR
AF:
0.00458
Gnomad ASJ
AF:
0.00576
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00290
Gnomad FIN
AF:
0.000377
Gnomad MID
AF:
0.0285
Gnomad NFE
AF:
0.00517
Gnomad OTH
AF:
0.00574
GnomAD3 exomes
AF:
0.00382
AC:
961
AN:
251380
Hom.:
3
AF XY:
0.00400
AC XY:
544
AN XY:
135874
show subpopulations
Gnomad AFR exome
AF:
0.000677
Gnomad AMR exome
AF:
0.00321
Gnomad ASJ exome
AF:
0.00655
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00317
Gnomad FIN exome
AF:
0.000556
Gnomad NFE exome
AF:
0.00549
Gnomad OTH exome
AF:
0.00652
GnomAD4 exome
AF:
0.00411
AC:
6014
AN:
1461808
Hom.:
31
Cov.:
32
AF XY:
0.00417
AC XY:
3031
AN XY:
727214
show subpopulations
Gnomad4 AFR exome
AF:
0.00105
Gnomad4 AMR exome
AF:
0.00335
Gnomad4 ASJ exome
AF:
0.00727
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00337
Gnomad4 FIN exome
AF:
0.000525
Gnomad4 NFE exome
AF:
0.00438
Gnomad4 OTH exome
AF:
0.00487
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00378
AC:
576
AN:
152326
Hom.:
4
Cov.:
32
AF XY:
0.00333
AC XY:
248
AN XY:
74486
show subpopulations
Gnomad4 AFR
AF:
0.000794
Gnomad4 AMR
AF:
0.00457
Gnomad4 ASJ
AF:
0.00576
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00290
Gnomad4 FIN
AF:
0.000377
Gnomad4 NFE
AF:
0.00517
Gnomad4 OTH
AF:
0.00568
Alfa
AF:
0.00450
Hom.:
2
Bravo
AF:
0.00421
Asia WGS
AF:
0.00115
AC:
4
AN:
3478
EpiCase
AF:
0.00752
EpiControl
AF:
0.00806

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 submitterclinical testingInvitaeJun 25, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.80
CADD
Benign
0.24
DANN
Benign
0.80

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.030
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs141567872; hg19: chr2-120221711; COSMIC: COSV50028080; API