chrX-47574013-G-A
Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_006950.3(SYN1):c.1971C>T(p.His657His) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000682 in 1,144,075 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 24 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_006950.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -17 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SYN1 | ENST00000295987.13 | c.1971C>T | p.His657His | synonymous_variant | Exon 12 of 13 | 2 | NM_006950.3 | ENSP00000295987.7 | ||
SYN1 | ENST00000340666.5 | c.1971C>T | p.His657His | synonymous_variant | Exon 12 of 13 | 1 | ENSP00000343206.4 | |||
SYN1 | ENST00000640721.1 | c.70+675C>T | intron_variant | Intron 1 of 1 | 5 | ENSP00000492857.1 |
Frequencies
GnomAD3 genomes AF: 0.0000355 AC: 4AN: 112671Hom.: 0 Cov.: 24 AF XY: 0.00 AC XY: 0AN XY: 34825
GnomAD4 exome AF: 0.0000718 AC: 74AN: 1031353Hom.: 0 Cov.: 32 AF XY: 0.0000725 AC XY: 24AN XY: 331075
GnomAD4 genome AF: 0.0000355 AC: 4AN: 112722Hom.: 0 Cov.: 24 AF XY: 0.00 AC XY: 0AN XY: 34886
ClinVar
Submissions by phenotype
not provided Benign:1
SYN1: BP4, BP7 -
Epilepsy, X-linked 1, with variable learning disabilities and behavior disorders Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at