rs75601897
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_017721.5(CC2D1A):c.1634T>C(p.Ile545Thr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00123 in 1,612,160 control chromosomes in the GnomAD database, including 16 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_017721.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00703 AC: 1071AN: 152250Hom.: 7 Cov.: 32
GnomAD3 exomes AF: 0.00170 AC: 415AN: 243750Hom.: 4 AF XY: 0.00128 AC XY: 170AN XY: 132656
GnomAD4 exome AF: 0.000630 AC: 919AN: 1459792Hom.: 9 Cov.: 33 AF XY: 0.000552 AC XY: 401AN XY: 726116
GnomAD4 genome AF: 0.00702 AC: 1070AN: 152368Hom.: 7 Cov.: 32 AF XY: 0.00682 AC XY: 508AN XY: 74512
ClinVar
Submissions by phenotype
not specified Benign:1
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Inborn genetic diseases Benign:1
This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at