11-2884860-GGGGGCCGGGGCCGGGGCC-GGGGGCC
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBS1BS2
The NM_001122630.2(CDKN1C):c.585_596delGGCCCCGGCCCC(p.Ala196_Pro199del) variant causes a disruptive inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0235 in 1,022,736 control chromosomes in the GnomAD database, including 474 homozygotes. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_001122630.2 disruptive_inframe_deletion
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: 0.0185 AC: 2643AN: 143212Hom.: 38 Cov.: 32
GnomAD4 exome AF: 0.0244 AC: 21423AN: 879430Hom.: 436 AF XY: 0.0242 AC XY: 10041AN XY: 415538
GnomAD4 genome AF: 0.0184 AC: 2642AN: 143306Hom.: 38 Cov.: 32 AF XY: 0.0176 AC XY: 1227AN XY: 69866
ClinVar
Submissions by phenotype
not specified Benign:5
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not provided Benign:4
CDKN1C: BS1, BS2 -
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The CDKN1C p.Ala213_Pro216del variant was not identified in the literature nor was it identified in Cosmic. The variant was identified in dbSNP (ID: rs759134767), ClinVar (classified as benign by Invitae, Prevention Genetics and EGL Genetic Diagnostics) and LOVD 3.0. The variant was identified in control databases in 415 of 25528 chromosomes (6 homozygous) at a frequency of 0.016257 increasing the likelihood this could be a low frequency benign variant (Genome Aggregation Database Feb 27, 2017). The variant was observed in the following populations: European (non-Finnish) in 344 of 13620 chromosomes (freq: 0.02526), Ashkenazi Jewish in 6 of 258 chromosomes (freq: 0.02326), Latino in 6 of 416 chromosomes (freq: 0.01442), Other in 10 of 752 chromosomes (freq: 0.0133), European (Finnish) in 6 of 962 chromosomes (freq: 0.006237) and African in 43 of 7844 chromosomes (freq: 0.005482); it was not observed in the East Asian or South Asian populations. The variant occurs outside the splicing consensus sequence and in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) do not predict a difference in splicing. This variant is an in-frame deletion resulting in the removal of the APAP residues between codons 213-216 in a non-conserved repeat region with unknown function. In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time although we would lean towards a more benign role for this variant. Therefore it is classified as likely benign. -
Beckwith-Wiedemann syndrome Benign:2
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at