8-144473424-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_145754.5(KIFC2):c.2491C>T(p.Pro831Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000109 in 1,556,606 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_145754.5 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KIFC2 | NM_001369769.2 | c.*35C>T | 3_prime_UTR_variant | 18/18 | ENST00000645548.2 | NP_001356698.1 | ||
FOXH1 | NM_003923.3 | c.*814G>A | 3_prime_UTR_variant | 3/3 | ENST00000377317.5 | NP_003914.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KIFC2 | ENST00000301332.3 | c.2491C>T | p.Pro831Ser | missense_variant | 17/17 | 1 | ENSP00000301332.2 | |||
KIFC2 | ENST00000645548.2 | c.*35C>T | 3_prime_UTR_variant | 18/18 | NM_001369769.2 | ENSP00000494595.1 | ||||
FOXH1 | ENST00000377317.5 | c.*814G>A | 3_prime_UTR_variant | 3/3 | 1 | NM_003923.3 | ENSP00000366534.4 | |||
KIFC2 | ENST00000643461.1 | n.2868C>T | non_coding_transcript_exon_variant | 17/17 |
Frequencies
GnomAD3 genomes AF: 0.0000657 AC: 10AN: 152168Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.00000498 AC: 7AN: 1404320Hom.: 0 Cov.: 34 AF XY: 0.00000288 AC XY: 2AN XY: 695186
GnomAD4 genome AF: 0.0000657 AC: 10AN: 152286Hom.: 0 Cov.: 33 AF XY: 0.0000537 AC XY: 4AN XY: 74456
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 20, 2023 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at