3-164979047-TA-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_001041.4(SI):c.*314del variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.118 in 180,896 control chromosomes in the GnomAD database, including 1,372 homozygotes. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.12 (1155 hom., cov: 30)
  • Exomes 𝑓: 0.11 (217 hom.)
• Consequence: SI NM_001041.4 3_prime_UTR
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.32

Genes affected

SI (HGNC:10856): (sucrase-isomaltase) This gene encodes a sucrase-isomaltase enzyme that is expressed in the intestinal brush border. The encoded protein is synthesized as a precursor protein that is cleaved by pancreatic proteases into two enzymatic subunits sucrase and isomaltase. These two subunits heterodimerize to form the sucrose-isomaltase complex. This complex is essential for the digestion of dietary carbohydrates including starch, sucrose and isomaltose. Mutations in this gene are the cause of congenital sucrase-isomaltase deficiency.[provided by RefSeq, Apr 2010]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 3-164979047-TA-T is Benign according to our data. Variant chr3-164979047-TA-T is described in ClinVar as [Likely_benign]. Clinvar id is 343995.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.147 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SI	NM_001041.4	c.*314del		3_prime_UTR_variant	48/48	ENST00000264382.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SI	ENST00000264382.8	c.*314del		3_prime_UTR_variant	48/48	1	NM_001041.4	P1

Frequencies

GnomAD3 genomes AF: 0.119 AC: 18058 AN: 151566 Hom.: 1154 Cov.: 30

Gnomad AFR AF: 0.134

Gnomad AMI AF: 0.205

Gnomad AMR AF: 0.0838

Gnomad ASJ AF: 0.116

Gnomad EAS AF: 0.0610

Gnomad SAS AF: 0.157

Gnomad FIN AF: 0.0585

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.128

Gnomad OTH AF: 0.119

GnomAD4 exome AF: 0.112 AC: 3278 AN: 29214 Hom.: 217 Cov.: 0 AF XY: 0.115 AC XY: 1822 AN XY: 15896

Gnomad4 AFR exome AF: 0.122

Gnomad4 AMR exome AF: 0.0614

Gnomad4 ASJ exome AF: 0.125

Gnomad4 EAS exome AF: 0.0581

Gnomad4 SAS exome AF: 0.156

Gnomad4 FIN exome AF: 0.0916

Gnomad4 NFE exome AF: 0.120

Gnomad4 OTH exome AF: 0.104

GnomAD4 genome AF: 0.119 AC: 18067 AN: 151682 Hom.: 1155 Cov.: 30 AF XY: 0.114 AC XY: 8474 AN XY: 74146

Gnomad4 AFR AF: 0.134

Gnomad4 AMR AF: 0.0837

Gnomad4 ASJ AF: 0.116

Gnomad4 EAS AF: 0.0609

Gnomad4 SAS AF: 0.157

Gnomad4 FIN AF: 0.0585

Gnomad4 NFE AF: 0.128

Gnomad4 OTH AF: 0.118

Alfa AF: 0.124 Hom.: 136

Bravo AF: 0.120

Asia WGS AF: 0.109 AC: 374 AN: 3432

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Sucrase-isomaltase deficiency Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

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Computational scores

Source: dbNSFP v4.3

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: rs145227457; hg19: chr3-164696835;