rs7152978
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001127713.1(ATL1):c.-140+60G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.994 in 152,216 control chromosomes in the GnomAD database, including 75,190 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001127713.1 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ATL1 | NM_001127713.1 | c.-140+60G>A | intron_variant | Intron 1 of 13 | NP_001121185.1 | |||
MAP4K5 | XM_047430893.1 | c.-109-1269C>T | intron_variant | Intron 2 of 33 | XP_047286849.1 | |||
MAP4K5 | XM_047430897.1 | c.-109-1269C>T | intron_variant | Intron 2 of 32 | XP_047286853.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ATL1 | ENST00000441560.6 | c.-140+60G>A | intron_variant | Intron 1 of 13 | 1 | ENSP00000413675.2 | ||||
ATL1 | ENST00000556478.3 | c.-140+554G>A | intron_variant | Intron 1 of 13 | 2 | ENSP00000501428.2 | ||||
MAP4K5 | ENST00000555216.5 | c.-94+9072C>T | intron_variant | Intron 2 of 8 | 4 | ENSP00000452289.1 | ||||
ATL1 | ENST00000682219.1 | n.740+60G>A | intron_variant | Intron 1 of 12 |
Frequencies
GnomAD3 genomes AF: 0.994 AC: 151168AN: 152098Hom.: 75133 Cov.: 30
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 1.00 AC: 2AN: 2Hom.: 1 AF XY: 1.00 AC XY: 2AN XY: 2
GnomAD4 genome AF: 0.994 AC: 151284AN: 152216Hom.: 75190 Cov.: 30 AF XY: 0.994 AC XY: 73991AN XY: 74412
ClinVar
Submissions by phenotype
not provided Benign:2
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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. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at