rs182460499
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS1
The NM_002582.4(PARN):c.1263-8T>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 0.00114 in 1,445,260 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 Likely benign (★★).
Frequency
Consequence
NM_002582.4 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000953 AC: 145AN: 152216Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000931 AC: 151AN: 162128Hom.: 0 AF XY: 0.00102 AC XY: 88AN XY: 86250
GnomAD4 exome AF: 0.00116 AC: 1497AN: 1292926Hom.: 1 Cov.: 18 AF XY: 0.00119 AC XY: 769AN XY: 643710
GnomAD4 genome AF: 0.000945 AC: 144AN: 152334Hom.: 0 Cov.: 32 AF XY: 0.000926 AC XY: 69AN XY: 74506
ClinVar
Submissions by phenotype
not provided Benign:4
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PARN: BP4 -
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not specified Benign:1
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Pulmonary fibrosis and/or bone marrow failure, Telomere-related, 4;C4225356:Dyskeratosis congenita, autosomal recessive 6 Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at