chr1-205169835-G-A
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_ModerateBP6_ModerateBS1BS2
The NM_015375.3(DSTYK):c.655-3C>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 0.000225 in 1,605,724 control chromosomes in the GnomAD database, including 8 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_015375.3 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000118 AC: 18AN: 152126Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000471 AC: 114AN: 241984Hom.: 1 AF XY: 0.000671 AC XY: 88AN XY: 131198
GnomAD4 exome AF: 0.000237 AC: 344AN: 1453480Hom.: 8 Cov.: 32 AF XY: 0.000353 AC XY: 255AN XY: 722356
GnomAD4 genome AF: 0.000118 AC: 18AN: 152244Hom.: 0 Cov.: 32 AF XY: 0.000175 AC XY: 13AN XY: 74440
ClinVar
Submissions by phenotype
Congenital anomalies of kidney and urinary tract 1 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Aug 15, 2013 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Aug 24, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at