rs375942071
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_001257.5(CDH13):c.1681+8C>G variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000289 in 1,597,068 control chromosomes in the GnomAD database, including 3 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 Likely benign (★).
Frequency
Consequence
NM_001257.5 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 |
---|---|---|---|---|---|---|---|
CDH13 | NM_001257.5 | c.1681+8C>G | splice_region_variant, intron_variant | ENST00000567109.6 | |||
CEDORA | XR_007065143.1 | n.142-12340G>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CDH13 | ENST00000567109.6 | c.1681+8C>G | splice_region_variant, intron_variant | 1 | NM_001257.5 | P1 | |||
CEDORA | ENST00000570056.2 | n.142-19259G>C | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.000191 AC: 29AN: 152208Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000566 AC: 138AN: 243748Hom.: 1 AF XY: 0.000614 AC XY: 81AN XY: 131964
GnomAD4 exome AF: 0.000299 AC: 432AN: 1444742Hom.: 3 Cov.: 30 AF XY: 0.000390 AC XY: 279AN XY: 715570
GnomAD4 genome ? AF: 0.000190 AC: 29AN: 152326Hom.: 0 Cov.: 32 AF XY: 0.000201 AC XY: 15AN XY: 74488
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at