19-49434053-G-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_020309.4(SLC17A7):c.638-7C>T variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000381 in 1,596,366 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_020309.4 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC17A7 | NM_020309.4 | c.638-7C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000221485.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC17A7 | ENST00000221485.8 | c.638-7C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_020309.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00167 AC: 254AN: 152136Hom.: 2 Cov.: 31
GnomAD3 exomes AF: 0.000509 AC: 124AN: 243454Hom.: 0 AF XY: 0.000370 AC XY: 49AN XY: 132356
GnomAD4 exome AF: 0.000244 AC: 352AN: 1444112Hom.: 0 Cov.: 28 AF XY: 0.000210 AC XY: 151AN XY: 719618
GnomAD4 genome AF: 0.00169 AC: 257AN: 152254Hom.: 2 Cov.: 31 AF XY: 0.00177 AC XY: 132AN XY: 74442
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Apr 06, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at