NM_001123385.2:c.4977-4G>T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001123385.2(BCOR):c.4977-4G>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.18 in 1,205,271 control chromosomes in the GnomAD database, including 14,154 homozygotes. There are 70,182 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001123385.2 splice_region, intron
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: 0.168 AC: 18570AN: 110308Hom.: 1282 Cov.: 22 AF XY: 0.153 AC XY: 4988AN XY: 32584
GnomAD3 exomes AF: 0.149 AC: 27117AN: 181988Hom.: 1467 AF XY: 0.154 AC XY: 10312AN XY: 67024
GnomAD4 exome AF: 0.181 AC: 197935AN: 1094910Hom.: 12874 Cov.: 31 AF XY: 0.181 AC XY: 65193AN XY: 360718
GnomAD4 genome AF: 0.168 AC: 18561AN: 110361Hom.: 1280 Cov.: 22 AF XY: 0.153 AC XY: 4989AN XY: 32647
ClinVar
Submissions by phenotype
not specified Benign:4
Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated disease phenotype. NOT Sanger confirmed. -
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Oculofaciocardiodental syndrome Benign:3
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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