X-140504323-A-AGCG
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP3BP6BS2
The NM_005634.3(SOX3):c.735_737dupCGC(p.Ala246dup) variant causes a disruptive inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000976 in 1,045,194 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 30 hemizygotes in GnomAD. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_005634.3 disruptive_inframe_insertion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000367 AC: 37AN: 100807Hom.: 0 Cov.: 23 AF XY: 0.000280 AC XY: 8AN XY: 28609
GnomAD3 exomes AF: 0.0000284 AC: 1AN: 35250Hom.: 0 AF XY: 0.000115 AC XY: 1AN XY: 8724
GnomAD4 exome AF: 0.0000678 AC: 64AN: 944350Hom.: 0 Cov.: 33 AF XY: 0.0000734 AC XY: 22AN XY: 299620
GnomAD4 genome AF: 0.000377 AC: 38AN: 100844Hom.: 0 Cov.: 23 AF XY: 0.000279 AC XY: 8AN XY: 28650
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:1
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Intellectual disability, X-linked, with panhypopituitarism Uncertain:1
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HP:0000157 (present);na:HP:0000465 (present);na:HP:0000767 (present);na:HP:0001876 (present);na:HP:0004322 (present);na:HP:0004808 (present);na:HP:0100543 (present) Uncertain:1
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SOX3-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at