16-21261270-G-C
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_001376256.1(CRYM):āc.864C>Gā(p.Thr288Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.437 in 1,611,502 control chromosomes in the GnomAD database, including 159,599 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Consequence
NM_001376256.1 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.521 AC: 79109AN: 151700Hom.: 22560 Cov.: 30
GnomAD3 exomes AF: 0.442 AC: 111014AN: 251314Hom.: 25858 AF XY: 0.439 AC XY: 59594AN XY: 135846
GnomAD4 exome AF: 0.428 AC: 624510AN: 1459684Hom.: 137011 Cov.: 34 AF XY: 0.428 AC XY: 310619AN XY: 726316
GnomAD4 genome AF: 0.522 AC: 79193AN: 151818Hom.: 22588 Cov.: 30 AF XY: 0.523 AC XY: 38791AN XY: 74188
ClinVar
Submissions by phenotype
not specified Benign:5
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Thr288Thr in Exon 09 of CRYM: This variant is not expected to have clinical sig nificance because it does not alter an amino acid residue, is not located within the splice consensus sequence, and has been identified in 41.4% (2906/7020) of European American chromosomes from a broad population by the NHLBI Exome Sequenc ing Project (http://evs.gs.washington.edu/EVS; dbSNP rs14122). -
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
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not provided Benign:2
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Autosomal dominant nonsyndromic hearing loss 40 Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at