chr17-28395709-C-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_080669.6(SLC46A1):c.*3947G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.574 in 585,312 control chromosomes in the GnomAD database, including 98,201 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_080669.6 3_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.590 AC: 89672AN: 151892Hom.: 26908 Cov.: 31
GnomAD4 exome AF: 0.568 AC: 246180AN: 433302Hom.: 71283 Cov.: 5 AF XY: 0.566 AC XY: 128351AN XY: 226822
GnomAD4 genome AF: 0.590 AC: 89724AN: 152010Hom.: 26918 Cov.: 31 AF XY: 0.585 AC XY: 43461AN XY: 74282
ClinVar
Submissions by phenotype
Congenital defect of folate absorption Benign:1
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at