16-30959145-T-C
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_014712.3(SETD1A):c.205T>C(p.Ser69Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000991 in 1,613,786 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S69T) has been classified as Uncertain significance.
Frequency
Consequence
NM_014712.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SETD1A | NM_014712.3 | c.205T>C | p.Ser69Pro | missense_variant | 3/19 | ENST00000262519.14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SETD1A | ENST00000262519.14 | c.205T>C | p.Ser69Pro | missense_variant | 3/19 | 1 | NM_014712.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000723 AC: 11AN: 152042Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251490Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135918
GnomAD4 exome AF: 0.00000342 AC: 5AN: 1461626Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 727156
GnomAD4 genome ? AF: 0.0000723 AC: 11AN: 152160Hom.: 0 Cov.: 31 AF XY: 0.0000672 AC XY: 5AN XY: 74410
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 10, 2021 | The c.205T>C (p.S69P) alteration is located in exon 3 (coding exon 2) of the SETD1A gene. This alteration results from a T to C substitution at nucleotide position 205, causing the serine (S) at amino acid position 69 to be replaced by a proline (P). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at