3-164979164-C-A

Variant names:

• chr3-164979164-C-A
• rs146143233
• NM_001041.4:c.*198G>T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BS1 BS2

The NM_001041.4(SI):​c.*198G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00314 in 548,436 control chromosomes in the GnomAD database, including 28 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.0083 (22 hom., cov: 32)
  • Exomes 𝑓: 0.0012 (6 hom.)
• Consequence: SI NM_001041.4 3_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.396

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 -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BP6: Variant 3-164979164-C-A is Benign according to our data. Variant chr3-164979164-C-A is described in ClinVar as [Benign]. Clinvar id is 900516.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS1: Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00832 (1262/151654) while in subpopulation AFR AF= 0.0291 (1207/41458). AF 95% confidence interval is 0.0277. There are 22 homozygotes in gnomad4. There are 597 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 22 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SI	NM_001041.4	c.*198G>T		3_prime_UTR_variant	Exon 48 of 48	ENST00000264382.8	NP_001032.2
SI	XM_047448735.1	c.*198G>T		3_prime_UTR_variant	Exon 49 of 49		XP_047304691.1
SI	XM_047448736.1	c.*198G>T		3_prime_UTR_variant	Exon 49 of 49		XP_047304692.1
SI	XM_011513078.3	c.*198G>T		3_prime_UTR_variant	Exon 47 of 47		XP_011511380.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SI	ENST00000264382	c.*198G>T		3_prime_UTR_variant	Exon 48 of 48	1	NM_001041.4	ENSP00000264382.3

Frequencies

GnomAD3 genomes AF: 0.00829 AC: 1256 AN: 151536 Hom.: 21 Cov.: 32

Gnomad AFR AF: 0.0290

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00244

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000207

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.0000443

Gnomad OTH AF: 0.00622

GnomAD4 exome AF: 0.00116 AC: 459 AN: 396782 Hom.: 6 Cov.: 2 AF XY: 0.000967 AC XY: 204 AN XY: 210986

Gnomad4 AFR exome AF: 0.0311

Gnomad4 AMR exome AF: 0.00135

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000109

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0000252

Gnomad4 OTH exome AF: 0.00263

GnomAD4 genome AF: 0.00832 AC: 1262 AN: 151654 Hom.: 22 Cov.: 32 AF XY: 0.00806 AC XY: 597 AN XY: 74098

Gnomad4 AFR AF: 0.0291

Gnomad4 AMR AF: 0.00244

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000443

Gnomad4 OTH AF: 0.00616

Alfa AF: 0.00727 Hom.: 1

Bravo AF: 0.00930

Asia WGS AF: 0.00116 AC: 4 AN: 3472

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Sucrase-isomaltase deficiency Benign:1

Apr 27, 2017

Illumina Laboratory Services, Illumina

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases was too high to be consistent with this variant causing disease. Therefore, this variant is classified as benign. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.5
DANN	Benign	0.37

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: rs146143233; hg19: chr3-164696952;