2-119453277-G-A

Position:

• chr2-119453277-G-A

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

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
• Clinical Significance: Benign criteria provided, single submitter B:1
• 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]

ACMG classification

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: 3313 AN: 152152 Hom.: 132 Cov.: 33

Gnomad AFR AF: 0.0722

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0119

Gnomad ASJ AF: 0.00548

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00124

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.00103

Gnomad OTH AF: 0.0210

GnomAD3 exomes AF: 0.00652 AC: 1639 AN: 251350 Hom.: 49 AF XY: 0.00498 AC XY: 677 AN XY: 135870

Gnomad AFR exome AF: 0.0748

Gnomad AMR exome AF: 0.00590

Gnomad ASJ exome AF: 0.00585

Gnomad EAS exome AF: 0.000109

Gnomad SAS exome AF: 0.000360

Gnomad FIN exome AF: 0.0000462

Gnomad NFE exome AF: 0.00106

Gnomad OTH exome AF: 0.00456

GnomAD4 exome AF: 0.00292 AC: 4212 AN: 1444408 Hom.: 107 Cov.: 28 AF XY: 0.00265 AC XY: 1909 AN XY: 719770

Gnomad4 AFR exome AF: 0.0762

Gnomad4 AMR exome AF: 0.00651

Gnomad4 ASJ exome AF: 0.00515

Gnomad4 EAS exome AF: 0.0000505

Gnomad4 SAS exome AF: 0.000431

Gnomad4 FIN exome AF: 0.0000374

Gnomad4 NFE exome AF: 0.000734

Gnomad4 OTH exome AF: 0.00634

GnomAD4 genome AF: 0.0218 AC: 3322 AN: 152270 Hom.: 132 Cov.: 33 AF XY: 0.0216 AC XY: 1612 AN XY: 74460

Gnomad4 AFR AF: 0.0722

Gnomad4 AMR AF: 0.0118

Gnomad4 ASJ AF: 0.00548

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00125

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00103

Gnomad4 OTH AF: 0.0208

Alfa AF: 0.0149 Hom.: 29

Bravo AF: 0.0258

Asia WGS AF: 0.00751 AC: 26 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Aug 15, 2017

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.34
DANN	Benign	0.66

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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

Other links and lift over

dbSNP: rs10496558; hg19: chr2-120210853;