3-164979164-C-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
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
Consequence
NM_001041.4 3_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
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
Frequencies
GnomAD3 genomes AF: 0.00829 AC: 1256AN: 151536Hom.: 21 Cov.: 32
GnomAD4 exome AF: 0.00116 AC: 459AN: 396782Hom.: 6 Cov.: 2 AF XY: 0.000967 AC XY: 204AN XY: 210986
GnomAD4 genome AF: 0.00832 AC: 1262AN: 151654Hom.: 22 Cov.: 32 AF XY: 0.00806 AC XY: 597AN XY: 74098
ClinVar
Submissions by phenotype
Sucrase-isomaltase deficiency Benign:1
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:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at