20-765779-GTATCTGCCC-G
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1
The NM_033409.4(SLC52A3):c.-14_-6delGGGCAGATA variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.264 in 1,608,422 control chromosomes in the GnomAD database, including 58,254 homozygotes. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_033409.4 5_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.276 AC: 41865AN: 151712Hom.: 5976 Cov.: 18
GnomAD3 exomes AF: 0.221 AC: 51450AN: 232958Hom.: 6367 AF XY: 0.217 AC XY: 27439AN XY: 126380
GnomAD4 exome AF: 0.263 AC: 383449AN: 1456592Hom.: 52277 AF XY: 0.259 AC XY: 187604AN XY: 724162
GnomAD4 genome AF: 0.276 AC: 41901AN: 151830Hom.: 5977 Cov.: 18 AF XY: 0.270 AC XY: 20061AN XY: 74216
ClinVar
Submissions by phenotype
not specified Benign:2
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c.-14_-6del in exon 2 of SLC52A3: This variant is not expected to have clinical significance because it has been identified in 33.2% (7594/22860) of African chr omosomes by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitut e.org/; dbSNP rs11467076). -
not provided Benign:1
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Brown-Vialetto-van Laere syndrome 1 Benign:1
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Progressive bulbar palsy of childhood Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at