2-189005473-T-G
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_000090.4(COL3A1):c.3039+16T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000786 in 1,591,614 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_000090.4 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: 0.00244 AC: 371AN: 152224Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00109 AC: 275AN: 251170Hom.: 0 AF XY: 0.000847 AC XY: 115AN XY: 135780
GnomAD4 exome AF: 0.000611 AC: 879AN: 1439272Hom.: 2 Cov.: 26 AF XY: 0.000582 AC XY: 418AN XY: 717678
GnomAD4 genome AF: 0.00244 AC: 372AN: 152342Hom.: 0 Cov.: 32 AF XY: 0.00224 AC XY: 167AN XY: 74496
ClinVar
Submissions by phenotype
not specified Benign:3
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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. -
not provided Benign:1
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Ehlers-Danlos syndrome, type 4 Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at