3-38478523-G-A
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBS1BS2
The NM_001106.4(ACVR2B):c.666+5G>A variant causes a splice region, intron change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0013 in 1,614,118 control chromosomes in the GnomAD database, including 21 homozygotes. In-silico tool predicts a benign outcome for this variant. 2/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001106.4 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ACVR2B | ENST00000352511.5 | c.666+5G>A | splice_region_variant, intron_variant | Intron 5 of 10 | 1 | NM_001106.4 | ENSP00000340361.3 | |||
ACVR2B | ENST00000461232.1 | n.4455+5G>A | splice_region_variant, intron_variant | Intron 4 of 9 | 1 | |||||
ACVR2B | ENST00000465020.5 | n.752+5G>A | splice_region_variant, intron_variant | Intron 4 of 9 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00699 AC: 1064AN: 152184Hom.: 9 Cov.: 32
GnomAD3 exomes AF: 0.00180 AC: 452AN: 251260Hom.: 6 AF XY: 0.00121 AC XY: 164AN XY: 135814
GnomAD4 exome AF: 0.000705 AC: 1031AN: 1461816Hom.: 13 Cov.: 33 AF XY: 0.000550 AC XY: 400AN XY: 727208
GnomAD4 genome AF: 0.00700 AC: 1066AN: 152302Hom.: 8 Cov.: 32 AF XY: 0.00663 AC XY: 494AN XY: 74470
ClinVar
Submissions by phenotype
not specified Benign:1
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Heterotaxy, visceral, 4, autosomal Benign:1
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not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at