chr19-10553955-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_023008.5(KRI1):c.2108C>T(p.Ser703Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000688 in 1,598,094 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/18 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S703P) has been classified as Likely benign.
Frequency
Consequence
NM_023008.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KRI1 | NM_023008.5 | c.2108C>T | p.Ser703Phe | missense_variant | 19/19 | ENST00000312962.12 | NP_075384.4 | |
KRI1 | XM_047439232.1 | c.2114C>T | p.Ser705Phe | missense_variant | 18/18 | XP_047295188.1 | ||
KRI1 | XM_011528190.3 | c.1772C>T | p.Ser591Phe | missense_variant | 18/18 | XP_011526492.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KRI1 | ENST00000312962.12 | c.2108C>T | p.Ser703Phe | missense_variant | 19/19 | 1 | NM_023008.5 | ENSP00000320917.9 |
Frequencies
GnomAD3 genomes AF: 0.0000328 AC: 5AN: 152222Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000852 AC: 2AN: 234836Hom.: 0 AF XY: 0.0000157 AC XY: 2AN XY: 127530
GnomAD4 exome AF: 0.00000415 AC: 6AN: 1445872Hom.: 0 Cov.: 29 AF XY: 0.00000696 AC XY: 5AN XY: 718178
GnomAD4 genome AF: 0.0000328 AC: 5AN: 152222Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74380
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 10, 2024 | The c.2126C>T (p.S709F) alteration is located in exon 19 (coding exon 19) of the KRI1 gene. This alteration results from a C to T substitution at nucleotide position 2126, causing the serine (S) at amino acid position 709 to be replaced by a phenylalanine (F). 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