17-8002739-A-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_000180.4(GUCY2D):c.-10+5A>G variant causes a splice donor 5th base, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 1 in 345,844 control chromosomes in the GnomAD database, including 172,917 homozygotes. In-silico tool predicts a benign outcome for this variant. 2/2 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_000180.4 splice_donor_5th_base, intron
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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GUCY2D | NM_000180.4 | c.-10+5A>G | splice_donor_5th_base_variant, intron_variant | ENST00000254854.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GUCY2D | ENST00000254854.5 | c.-10+5A>G | splice_donor_5th_base_variant, intron_variant | 1 | NM_000180.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 1.00 AC: 152139AN: 152140Hom.: 76069 Cov.: 32
GnomAD4 exome AF: 1.00 AC: 193584AN: 193588Hom.: 96790 Cov.: 0 AF XY: 1.00 AC XY: 99827AN XY: 99828
GnomAD4 genome ? AF: 1.00 AC: 152255AN: 152256Hom.: 76127 Cov.: 32 AF XY: 1.00 AC XY: 74426AN XY: 74426
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 19, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at