X-119087094-G-A
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_001394962.1(KIAA1210):c.3608C>T(p.Ser1203Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00021 in 1,209,840 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 87 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001394962.1 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KIAA1210 | NM_001394962.1 | c.3608C>T | p.Ser1203Phe | missense_variant | 9/12 | ENST00000691062.1 | NP_001381891.1 | |
KIAA1210 | NM_020721.1 | c.4136C>T | p.Ser1379Phe | missense_variant | 11/14 | NP_065772.1 | ||
KIAA1210 | XM_017029688.3 | c.3653C>T | p.Ser1218Phe | missense_variant | 9/12 | XP_016885177.1 | ||
KIAA1210 | XM_017029689.3 | c.3455C>T | p.Ser1152Phe | missense_variant | 8/11 | XP_016885178.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KIAA1210 | ENST00000691062.1 | c.3608C>T | p.Ser1203Phe | missense_variant | 9/12 | NM_001394962.1 | ENSP00000510348.1 | |||
KIAA1210 | ENST00000402510.2 | c.4136C>T | p.Ser1379Phe | missense_variant | 11/14 | 5 | ENSP00000384670.2 |
Frequencies
GnomAD3 genomes AF: 0.000214 AC: 24AN: 111983Hom.: 0 Cov.: 23 AF XY: 0.0000879 AC XY: 3AN XY: 34135
GnomAD3 exomes AF: 0.000237 AC: 43AN: 181376Hom.: 0 AF XY: 0.000252 AC XY: 17AN XY: 67364
GnomAD4 exome AF: 0.000210 AC: 230AN: 1097803Hom.: 0 Cov.: 32 AF XY: 0.000231 AC XY: 84AN XY: 363237
GnomAD4 genome AF: 0.000214 AC: 24AN: 112037Hom.: 0 Cov.: 23 AF XY: 0.0000877 AC XY: 3AN XY: 34199
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 17, 2022 | The c.4136C>T (p.S1379F) alteration is located in exon 11 (coding exon 11) of the KIAA1210 gene. This alteration results from a C to T substitution at nucleotide position 4136, causing the serine (S) at amino acid position 1379 to be replaced by a phenylalanine (F). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Nov 01, 2022 | KIAA1210: BP4, BS2 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at