chr11-62856389-A-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The ENST00000377890.6(SLC3A2):c.112+8A>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00029 in 1,598,820 control chromosomes in the GnomAD database, including 1 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
ENST00000377890.6 splice_region, 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 |
---|---|---|---|---|---|---|---|
SLC3A2 | NM_001012662.3 | c.112+8A>T | splice_region_variant, intron_variant | ||||
SLC3A2 | NM_001012664.3 | c.112+8A>T | splice_region_variant, intron_variant | ||||
SLC3A2 | NM_002394.6 | c.112+8A>T | splice_region_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC3A2 | ENST00000377889.6 | c.112+8A>T | splice_region_variant, intron_variant | 1 | |||||
SLC3A2 | ENST00000377890.6 | c.112+8A>T | splice_region_variant, intron_variant | 1 | |||||
SLC3A2 | ENST00000681569.1 | c.120A>T | p.Gly40= | synonymous_variant | 1/12 |
Frequencies
GnomAD3 genomes ? AF: 0.00128 AC: 195AN: 152186Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000388 AC: 96AN: 247696Hom.: 0 AF XY: 0.000298 AC XY: 40AN XY: 134138
GnomAD4 exome AF: 0.000185 AC: 267AN: 1446516Hom.: 1 Cov.: 30 AF XY: 0.000174 AC XY: 125AN XY: 717170
GnomAD4 genome ? AF: 0.00129 AC: 196AN: 152304Hom.: 0 Cov.: 33 AF XY: 0.00119 AC XY: 89AN XY: 74484
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jun 08, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at