7-142942882-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_000420.3(KEL):c.1934C>T(p.Ala645Val) variant causes a missense change. The variant allele was found at a frequency of 0.0000613 in 1,614,128 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Affects (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A645E) has been classified as Uncertain significance.
Frequency
Consequence
NM_000420.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KEL | NM_000420.3 | c.1934C>T | p.Ala645Val | missense_variant | 17/19 | ENST00000355265.7 | |
KEL | XM_005249993.2 | c.1970C>T | p.Ala657Val | missense_variant | 17/19 | ||
KEL | XM_047420357.1 | c.1823C>T | p.Ala608Val | missense_variant | 16/18 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KEL | ENST00000355265.7 | c.1934C>T | p.Ala645Val | missense_variant | 17/19 | 1 | NM_000420.3 | P1 | |
KEL | ENST00000470850.1 | n.234C>T | non_coding_transcript_exon_variant | 3/4 | 2 | ||||
KEL | ENST00000478969.1 | n.273C>T | non_coding_transcript_exon_variant | 1/2 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000854 AC: 13AN: 152146Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000876 AC: 22AN: 251210Hom.: 0 AF XY: 0.0000663 AC XY: 9AN XY: 135776
GnomAD4 exome AF: 0.0000588 AC: 86AN: 1461864Hom.: 0 Cov.: 33 AF XY: 0.0000454 AC XY: 33AN XY: 727242
GnomAD4 genome AF: 0.0000854 AC: 13AN: 152264Hom.: 0 Cov.: 33 AF XY: 0.0000806 AC XY: 6AN XY: 74444
ClinVar
Submissions by phenotype
Kell blood group system Other:1
Affects, no assertion criteria provided | research | Australian Red Cross Blood Service | Jul 01, 2021 | has KEL*01.01 allele at heterozygous level but serology is K neg with some antisera and K pos with others. This rare nucleotide substitution (c.1934C>T) may be impacting K expression. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at