chr11-2445119-G-A
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_000218.3(KCNQ1):c.21G>A(p.Pro7=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000418 in 957,068 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. P7P) has been classified as Likely benign.
Frequency
Consequence
NM_000218.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KCNQ1 | NM_000218.3 | c.21G>A | p.Pro7= | synonymous_variant | 1/16 | ENST00000155840.12 | |
KCNQ1 | NM_001406836.1 | c.21G>A | p.Pro7= | synonymous_variant | 1/15 | ||
KCNQ1 | NM_001406838.1 | c.21G>A | p.Pro7= | synonymous_variant | 1/11 | ||
KCNQ1 | NM_001406837.1 | c.-342G>A | 5_prime_UTR_variant | 1/17 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KCNQ1 | ENST00000155840.12 | c.21G>A | p.Pro7= | synonymous_variant | 1/16 | 1 | NM_000218.3 | P1 | |
KCNQ1 | ENST00000646564.2 | c.21G>A | p.Pro7= | synonymous_variant | 1/11 | ||||
KCNQ1 | ENST00000496887.7 | c.24-264G>A | intron_variant | 5 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome AF: 0.00000418 AC: 4AN: 957068Hom.: 0 Cov.: 30 AF XY: 0.00000221 AC XY: 1AN XY: 453260
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Long QT syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | May 27, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at