8-144517095-C-T
Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_004260.4(RECQL4):c.309G>A(p.Pro103Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00561 in 1,612,434 control chromosomes in the GnomAD database, including 58 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. P103P) has been classified as Likely benign.
Frequency
Consequence
NM_004260.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -17 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00549 AC: 836AN: 152268Hom.: 5 Cov.: 34
GnomAD3 exomes AF: 0.00655 AC: 1616AN: 246722Hom.: 15 AF XY: 0.00654 AC XY: 881AN XY: 134674
GnomAD4 exome AF: 0.00562 AC: 8212AN: 1460048Hom.: 53 Cov.: 31 AF XY: 0.00549 AC XY: 3986AN XY: 726300
GnomAD4 genome AF: 0.00549 AC: 836AN: 152386Hom.: 5 Cov.: 34 AF XY: 0.00648 AC XY: 483AN XY: 74516
ClinVar
Submissions by phenotype
not provided Benign:4
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RECQL4: BP4, BP7, BS2 -
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not specified Benign:2
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Inborn genetic diseases Benign:1
This alteration is classified as likely 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. -
Rothmund-Thomson syndrome type 2 Benign:1
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Baller-Gerold syndrome Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at