rs75716989

Variant names:

• chr2-119440195-G-A
• rs75716989
• NM_002980.3:c.1245C>T

Your query was ambiguous. Multiple possible variants found:

• chr2-119440195-G-A
• chr2-119440195-G-T

Variant summary

Our verdict is Benign. The variant received -21 ACMG points: 0P and 21B. BP4_Strong BP6_Very_Strong BP7 BA1

The NM_002980.3(SCTR):​c.1245C>T​(p.Pro415Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00305 in 1,614,002 control chromosomes in the GnomAD database, including 133 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.016 (69 hom., cov: 33)
  • Exomes 𝑓: 0.0017 (64 hom.)
• Consequence: SCTR NM_002980.3 synonymous
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.793
• Publications: 1 publications found

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

Our verdict: Benign. The variant received -21 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BP6: Variant 2-119440195-G-A is Benign according to our data. Variant chr2-119440195-G-A is described in ClinVar as Benign. ClinVar VariationId is 785976.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BP7: Synonymous conserved (PhyloP=-0.793 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0537 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002980.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SCTR	NM_002980.3	MANE Select	c.1245C>T	p.Pro415Pro	synonymous	Exon 13 of 13	NP_002971.2	P47872

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SCTR	ENST00000019103.8	TSL:1 MANE Select	c.1245C>T	p.Pro415Pro	synonymous	Exon 13 of 13	ENSP00000019103.6	P47872
	SCTR	ENST00000903274.1		c.1440C>T	p.Pro480Pro	synonymous	Exon 15 of 15	ENSP00000573333.1
	SCTR	ENST00000903275.1		c.1260C>T	p.Pro420Pro	synonymous	Exon 13 of 13	ENSP00000573334.1

Frequencies

GnomAD3 genomes AF: 0.0160 AC: 2442 AN: 152206 Hom.: 68 Cov.: 33

Gnomad AFR AF: 0.0554

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00615

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000620

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.000250

Gnomad OTH AF: 0.0134

GnomAD2 exomes AF: 0.00435 AC: 1091 AN: 250894 AF XY: 0.00338

Gnomad AFR exome AF: 0.0573

Gnomad AMR exome AF: 0.00327

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.0000544

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000273

Gnomad OTH exome AF: 0.00213

GnomAD4 exome AF: 0.00168 AC: 2462 AN: 1461678 Hom.: 64 Cov.: 34 AF XY: 0.00148 AC XY: 1079 AN XY: 727148

African (AFR) AF: 0.0567 AC: 1898 AN: 33474

American (AMR) AF: 0.00351 AC: 157 AN: 44712

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 26132

East Asian (EAS) AF: 0.000227 AC: 9 AN: 39686

South Asian (SAS) AF: 0.000116 AC: 10 AN: 86246

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 53396

Middle Eastern (MID) AF: 0.00298 AC: 17 AN: 5702

European-Non Finnish (NFE) AF: 0.0000935 AC: 104 AN: 1111958

Other (OTH) AF: 0.00442 AC: 267 AN: 60372

GnomAD4 genome AF: 0.0161 AC: 2453 AN: 152324 Hom.: 69 Cov.: 33 AF XY: 0.0155 AC XY: 1156 AN XY: 74484

African (AFR) AF: 0.0555 AC: 2309 AN: 41570

American (AMR) AF: 0.00614 AC: 94 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5178

South Asian (SAS) AF: 0.000621 AC: 3 AN: 4832

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10626

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.000250 AC: 17 AN: 68028

Other (OTH) AF: 0.0133 AC: 28 AN: 2112

Alfa AF: 0.00681 Hom.: 17

Bravo AF: 0.0181

EpiCase AF: 0.000327

EpiControl AF: 0.000415

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
-	-	2	not provided (2)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	0.30
DANN	Benign	0.60
PhyloP100		-0.79
Mutation Taster		=99/1	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.050		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs75716989; hg19: chr2-120197771;