11-626520-C-T

Variant names:

• chr11-626520-C-T
• rs1188015685
• NM_021920.4:c.277G>A

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_021920.4(SCT):​c.277G>A​(p.Asp93Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000711 in 1,406,292 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/23 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 7.1e-7 (0 hom.)
• Consequence: SCT NM_021920.4 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: -1.53

Genes affected

SCT (HGNC:10607): (secretin) This gene encodes a member of the glucagon family of peptides. The encoded preproprotein is secreted by endocrine S cells in the proximal small intestinal mucosa as a prohormone, then proteolytically processed to generate the mature peptide hormone. The release of this active peptide hormone is stimulated by either fatty acids or acidic pH in the duodenum. This hormone stimulates the secretion of bile and bicarbonate in the duodenum, pancreatic and biliary ducts. [provided by RefSeq, Feb 2016]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.06337577).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SCT	NM_021920.4	c.277G>A	p.Asp93Asn	missense_variant	Exon 4 of 4	ENST00000176195.4	NP_068739.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SCT	ENST00000176195.4	c.277G>A	p.Asp93Asn	missense_variant	Exon 4 of 4	1	NM_021920.4	ENSP00000176195.3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD2 exomes AF: 0.00 AC: 0 AN: 165216 AF XY: 0.00

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 7.11e-7 AC: 1 AN: 1406292 Hom.: 0 Cov.: 32 AF XY: 0.00000144 AC XY: 1 AN XY: 694280

Gnomad4 AFR exome AF: 0.00 AC: 0 AN: 31974

Gnomad4 AMR exome AF: 0.00 AC: 0 AN: 36578

Gnomad4 ASJ exome AF: 0.00 AC: 0 AN: 25244

Gnomad4 EAS exome AF: 0.00 AC: 0 AN: 36476

Gnomad4 SAS exome AF: 0.00 AC: 0 AN: 79658

Gnomad4 FIN exome AF: 0.00 AC: 0 AN: 49516

Gnomad4 NFE exome AF: 9.23e-7 AC: 1 AN: 1082982

Gnomad4 Remaining exome AF: 0.00 AC: 0 AN: 58278

GnomAD4 genome Cov.: 32

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Nov 17, 2022

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.277G>A (p.D93N) alteration is located in exon 4 (coding exon 4) of the SCT gene. This alteration results from a G to A substitution at nucleotide position 277, causing the aspartic acid (D) at amino acid position 93 to be replaced by an asparagine (N). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.12
BayesDel_addAF	Benign	-0.29	T
BayesDel_noAF	Benign	-0.66
CADD	Benign	9.3
DANN	Uncertain	0.99
DEOGEN2	Benign	0.15	T
Eigen	Benign	-1.1
Eigen_PC	Benign	-1.2
FATHMM_MKL	Benign	0.041	N
M_CAP	Benign	0.015	T
MetaRNN	Benign	0.063	T
MetaSVM	Benign	-0.97	T
MutationAssessor	Benign	1.6	L
PrimateAI	Benign	0.42	T
PROVEAN	Benign	-1.4	N
REVEL	Benign	0.027
Sift	Benign	0.071	T
Sift4G	Pathogenic	0.0	D
Polyphen		0.017	B
Vest4		0.10
MutPred		0.29		Gain of glycosylation at T95 (P = 0.1072);
MVP		0.24
MPC		0.25
ClinPred		0.070	T
GERP RS		1.1
Varity_R		0.041
gMVP		0.093
Mutation Taster		=97/3	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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: rs1188015685; hg19: chr11-626520;