1-17622992-G-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_018125.4(ARHGEF10L):c.1021-4G>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00435 in 1,610,694 control chromosomes in the GnomAD database, including 281 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 Benign (★).
Frequency
Consequence
NM_018125.4 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ARHGEF10L | ENST00000361221.8 | c.1021-4G>T | splice_region_variant, intron_variant | Intron 11 of 28 | 1 | NM_018125.4 | ENSP00000355060.3 | |||
ARHGEF10L | ENST00000375415.5 | c.904-4G>T | splice_region_variant, intron_variant | Intron 9 of 26 | 1 | ENSP00000364564.1 | ||||
ARHGEF10L | ENST00000375408.7 | c.355-4G>T | splice_region_variant, intron_variant | Intron 3 of 19 | 5 | ENSP00000364557.3 | ||||
ARHGEF10L | ENST00000469726.5 | n.1301-4G>T | splice_region_variant, intron_variant | Intron 3 of 19 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0234 AC: 3569AN: 152196Hom.: 146 Cov.: 33
GnomAD3 exomes AF: 0.00609 AC: 1505AN: 247112Hom.: 59 AF XY: 0.00450 AC XY: 602AN XY: 133854
GnomAD4 exome AF: 0.00235 AC: 3433AN: 1458380Hom.: 134 Cov.: 31 AF XY: 0.00199 AC XY: 1443AN XY: 725474
GnomAD4 genome AF: 0.0235 AC: 3579AN: 152314Hom.: 147 Cov.: 33 AF XY: 0.0226 AC XY: 1687AN XY: 74482
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | May 31, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at