22-39381817-C-CCAA
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 1P and 10B. PM4_SupportingBP6_ModerateBA1
The NM_004711.5(SYNGR1):c.607_608insACA(p.Pro202_Thr203insAsn) variant causes a disruptive inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.713 in 1,612,432 control chromosomes in the GnomAD database, including 415,053 homozygotes. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_004711.5 disruptive_inframe_insertion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.759 AC: 115118AN: 151640Hom.: 44572 Cov.: 0
GnomAD3 exomes AF: 0.757 AC: 188057AN: 248486Hom.: 72691 AF XY: 0.751 AC XY: 101362AN XY: 135042
GnomAD4 exome AF: 0.708 AC: 1033689AN: 1460674Hom.: 370426 Cov.: 37 AF XY: 0.708 AC XY: 514841AN XY: 726664
GnomAD4 genome AF: 0.759 AC: 115228AN: 151758Hom.: 44627 Cov.: 0 AF XY: 0.763 AC XY: 56604AN XY: 74138
ClinVar
Submissions by phenotype
Schizophrenia Benign:1
The c.607_608insACA variant in SYNGR1 has been reported in at least 1 individual with schizophrenia (PMID: 17049558), and has been identified in >99% of East Asian chromosomes and 34864 homozygotes by ExAC (http://gnomad.broadinstitute.org/). In summary, this variant meets criteria to be classified as benign for schizophrenia. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at