chr1-110061017-G-C
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_006492.3(ALX3):c.748C>G(p.Pro250Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000623 in 1,610,442 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_006492.3 missense
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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ALX3 | NM_006492.3 | c.748C>G | p.Pro250Ala | missense_variant | 4/4 | ENST00000647563.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ALX3 | ENST00000647563.2 | c.748C>G | p.Pro250Ala | missense_variant | 4/4 | NM_006492.3 | P1 | ||
ENST00000554749.1 | n.2678G>C | non_coding_transcript_exon_variant | 1/1 | ||||||
ALX3 | ENST00000649954.1 | c.319C>G | p.Pro107Ala | missense_variant | 3/3 | ||||
STRIP1 | ENST00000473429.5 | n.4213+6215G>C | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00333 AC: 506AN: 152154Hom.: 3 Cov.: 33
GnomAD3 exomes AF: 0.000655 AC: 155AN: 236576Hom.: 0 AF XY: 0.000486 AC XY: 63AN XY: 129698
GnomAD4 exome AF: 0.000341 AC: 497AN: 1458170Hom.: 2 Cov.: 34 AF XY: 0.000303 AC XY: 220AN XY: 725086
GnomAD4 genome ? AF: 0.00333 AC: 507AN: 152272Hom.: 3 Cov.: 33 AF XY: 0.00326 AC XY: 243AN XY: 74470
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Jul 24, 2015 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 10, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at