NM_001365999.1:c.5535T>G
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001365999.1(SZT2):āc.5535T>Gā(p.Ser1845Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00262 in 1,613,606 control chromosomes in the GnomAD database, including 95 homozygotes. In-silico tool predicts a benign outcome for this variant. 11/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Consequence
NM_001365999.1 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: 0.0141 AC: 2138AN: 151776Hom.: 51 Cov.: 32
GnomAD3 exomes AF: 0.00360 AC: 902AN: 250470Hom.: 13 AF XY: 0.00263 AC XY: 356AN XY: 135424
GnomAD4 exome AF: 0.00142 AC: 2078AN: 1461712Hom.: 42 Cov.: 33 AF XY: 0.00126 AC XY: 918AN XY: 727148
GnomAD4 genome AF: 0.0141 AC: 2149AN: 151894Hom.: 53 Cov.: 32 AF XY: 0.0134 AC XY: 997AN XY: 74190
ClinVar
Submissions by phenotype
not provided Benign:4
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not specified Benign:1
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Developmental and epileptic encephalopathy, 18 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. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at