rs760310751
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_002473.6(MYH9):c.3101-5T>C variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000105 in 1,613,572 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 Likely benign (★★).
Frequency
Consequence
NM_002473.6 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MYH9 | NM_002473.6 | c.3101-5T>C | splice_region_variant, intron_variant | Intron 24 of 40 | ENST00000216181.11 | NP_002464.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MYH9 | ENST00000216181.11 | c.3101-5T>C | splice_region_variant, intron_variant | Intron 24 of 40 | 1 | NM_002473.6 | ENSP00000216181.6 | |||
MYH9 | ENST00000685801.1 | c.3164-5T>C | splice_region_variant, intron_variant | Intron 25 of 41 | ENSP00000510688.1 | |||||
MYH9 | ENST00000459960.1 | n.305T>C | non_coding_transcript_exon_variant | Exon 1 of 2 | 2 | |||||
MYH9 | ENST00000691109.1 | n.3396-5T>C | splice_region_variant, intron_variant | Intron 18 of 34 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152236Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000798 AC: 2AN: 250622Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135598
GnomAD4 exome AF: 0.0000103 AC: 15AN: 1461336Hom.: 0 Cov.: 31 AF XY: 0.0000138 AC XY: 10AN XY: 726992
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152236Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74378
ClinVar
Submissions by phenotype
not specified 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