chr5-5187717-T-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_139056.4(ADAMTS16):c.964-8T>A variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000223 in 1,603,808 control chromosomes in the GnomAD database, including 4 homozygotes. 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_139056.4 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ADAMTS16 | NM_139056.4 | c.964-8T>A | splice_region_variant, intron_variant | Intron 5 of 22 | ENST00000274181.7 | NP_620687.2 | ||
ADAMTS16 | XM_047416874.1 | c.964-8T>A | splice_region_variant, intron_variant | Intron 5 of 21 | XP_047272830.1 | |||
ADAMTS16 | XM_047416875.1 | c.964-8T>A | splice_region_variant, intron_variant | Intron 5 of 19 | XP_047272831.1 | |||
ADAMTS16 | NR_136935.2 | n.1102-8T>A | splice_region_variant, intron_variant | Intron 5 of 21 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ADAMTS16 | ENST00000274181.7 | c.964-8T>A | splice_region_variant, intron_variant | Intron 5 of 22 | 2 | NM_139056.4 | ENSP00000274181.7 | |||
ADAMTS16 | ENST00000511368.5 | c.964-8T>A | splice_region_variant, intron_variant | Intron 5 of 10 | 1 | ENSP00000421631.1 | ||||
ADAMTS16 | ENST00000433402.2 | n.964-8T>A | splice_region_variant, intron_variant | Intron 5 of 19 | 1 |
Frequencies
GnomAD3 genomes AF: 0.00120 AC: 182AN: 152212Hom.: 1 Cov.: 33
GnomAD3 exomes AF: 0.000270 AC: 67AN: 248422Hom.: 0 AF XY: 0.000148 AC XY: 20AN XY: 134754
GnomAD4 exome AF: 0.000121 AC: 175AN: 1451478Hom.: 3 Cov.: 28 AF XY: 0.0000899 AC XY: 65AN XY: 722734
GnomAD4 genome AF: 0.00119 AC: 182AN: 152330Hom.: 1 Cov.: 33 AF XY: 0.00121 AC XY: 90AN XY: 74484
ClinVar
Submissions by phenotype
not provided Benign:1
ADAMTS16: BP4 -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at