1-17373238-G-A
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBS1_Supporting
The NM_207421.4(PADI6):c.294+5G>A 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 0.0000595 in 1,613,262 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_207421.4 splice_donor_5th_base, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PADI6 | NM_207421.4 | c.294+5G>A | splice_donor_5th_base_variant, intron_variant | ENST00000619609.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PADI6 | ENST00000619609.1 | c.294+5G>A | splice_donor_5th_base_variant, intron_variant | 1 | NM_207421.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000986 AC: 15AN: 152202Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000246 AC: 61AN: 248432Hom.: 0 AF XY: 0.000289 AC XY: 39AN XY: 134778
GnomAD4 exome AF: 0.0000554 AC: 81AN: 1460942Hom.: 0 Cov.: 31 AF XY: 0.0000619 AC XY: 45AN XY: 726648
GnomAD4 genome AF: 0.0000985 AC: 15AN: 152320Hom.: 0 Cov.: 32 AF XY: 0.0000806 AC XY: 6AN XY: 74472
ClinVar
Submissions by phenotype
Preimplantation embryonic lethality 2 Uncertain:1
Uncertain significance, criteria provided, single submitter | case-control | Wang Lab, The Lab for Reproductive Genetics, Fudan University | Nov 01, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at