rs10406920
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000598188.6(BABAM1):c.787-6C>T variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.173 in 1,608,172 control chromosomes in the GnomAD database, including 25,508 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
ENST00000598188.6 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
BABAM1 | NM_014173.4 | c.787-6C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000598188.6 | NP_054892.2 | |||
BABAM1 | NM_001033549.3 | c.787-6C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | NP_001028721.1 | ||||
BABAM1 | NM_001288756.2 | c.787-6C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | NP_001275685.1 | ||||
BABAM1 | NM_001288757.2 | c.562-6C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | NP_001275686.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
BABAM1 | ENST00000598188.6 | c.787-6C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_014173.4 | ENSP00000471605 | P1 |
Frequencies
GnomAD3 genomes AF: 0.172 AC: 26092AN: 152062Hom.: 2411 Cov.: 32
GnomAD3 exomes AF: 0.147 AC: 35422AN: 240154Hom.: 3021 AF XY: 0.150 AC XY: 19548AN XY: 130652
GnomAD4 exome AF: 0.173 AC: 252053AN: 1455992Hom.: 23098 Cov.: 32 AF XY: 0.172 AC XY: 124619AN XY: 723778
GnomAD4 genome AF: 0.171 AC: 26089AN: 152180Hom.: 2410 Cov.: 32 AF XY: 0.170 AC XY: 12611AN XY: 74398
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at