1-32014159-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_006559.3(KHDRBS1):c.164C>T(p.Ala55Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000453 in 1,303,172 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 Uncertain significance (★).
Frequency
Consequence
NM_006559.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KHDRBS1 | ENST00000327300.12 | c.164C>T | p.Ala55Val | missense_variant | Exon 1 of 9 | 1 | NM_006559.3 | ENSP00000313829.7 | ||
KHDRBS1 | ENST00000492989.1 | c.164C>T | p.Ala55Val | missense_variant | Exon 1 of 8 | 1 | ENSP00000417731.1 | |||
KHDRBS1 | ENST00000307714.12 | n.234C>T | non_coding_transcript_exon_variant | Exon 1 of 9 | 1 | |||||
KHDRBS1 | ENST00000484270.2 | n.-23C>T | upstream_gene_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000724 AC: 11AN: 151920Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.0000417 AC: 48AN: 1151252Hom.: 0 Cov.: 31 AF XY: 0.0000434 AC XY: 24AN XY: 553356
GnomAD4 genome AF: 0.0000724 AC: 11AN: 151920Hom.: 0 Cov.: 32 AF XY: 0.0000674 AC XY: 5AN XY: 74236
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.164C>T (p.A55V) alteration is located in exon 1 (coding exon 1) of the KHDRBS1 gene. This alteration results from a C to T substitution at nucleotide position 164, causing the alanine (A) at amino acid position 55 to be replaced by a valine (V). 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