11-126424922-G-A
Variant summary
Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_032531.4(KIRREL3):c.1995C>T(p.Gly665Gly) variant causes a synonymous change. The variant allele was found at a frequency of 0.636 in 1,604,440 control chromosomes in the GnomAD database, including 327,436 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_032531.4 synonymous
Scores
Clinical Significance
Conservation
Publications
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ACMG classification
Our verdict: Benign. The variant received -20 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KIRREL3 | ENST00000525144.7 | c.1995C>T | p.Gly665Gly | synonymous_variant | Exon 17 of 17 | 1 | NM_032531.4 | ENSP00000435466.2 | ||
KIRREL3 | ENST00000529097.6 | c.1959C>T | p.Gly653Gly | synonymous_variant | Exon 16 of 16 | 1 | ENSP00000434081.2 | |||
ST3GAL4 | ENST00000524834.5 | n.630-15264G>A | intron_variant | Intron 6 of 6 | 2 |
Frequencies
GnomAD3 genomes AF: 0.668 AC: 101646AN: 152066Hom.: 34299 Cov.: 35 show subpopulations
GnomAD2 exomes AF: 0.661 AC: 162630AN: 245874 AF XY: 0.660 show subpopulations
GnomAD4 exome AF: 0.633 AC: 919027AN: 1452256Hom.: 293120 Cov.: 64 AF XY: 0.634 AC XY: 456527AN XY: 720542 show subpopulations
GnomAD4 genome AF: 0.668 AC: 101714AN: 152184Hom.: 34316 Cov.: 35 AF XY: 0.671 AC XY: 49937AN XY: 74394 show subpopulations
ClinVar
Submissions by phenotype
not provided Benign:2
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not specified Benign:1
Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated disease phenotype. NOT Sanger confirmed. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at