8-144474183-G-A
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_001369769.2(KIFC2):c.*794G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000494 in 1,386,196 control chromosomes in the GnomAD database, including 6 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.00049 ( 1 hom., cov: 32)
Exomes 𝑓: 0.00050 ( 5 hom. )
Consequence
KIFC2
NM_001369769.2 3_prime_UTR
NM_001369769.2 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.769
Genes affected
KIFC2 (HGNC:29530): (kinesin family member C2) Predicted to enable microtubule binding activity and microtubule motor activity. Predicted to be involved in microtubule-based movement and mitotic spindle assembly. Predicted to be located in cytoplasm. Predicted to be part of kinesin complex. Predicted to be active in microtubule cytoskeleton and nucleus. [provided by Alliance of Genome Resources, Apr 2022]
FOXH1 (HGNC:3814): (forkhead box H1) FOXH1 encodes a human homolog of Xenopus forkhead activin signal transducer-1. FOXH1 protein binds SMAD2 and activates an activin response element via binding the DNA motif TGT(G/T)(T/G)ATT. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BP6
Variant 8-144474183-G-A is Benign according to our data. Variant chr8-144474183-G-A is described in ClinVar as [Benign]. Clinvar id is 362276.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population eas. gnomad4_exome allele frequency = 0.000495 (611/1233936) while in subpopulation EAS AF= 0.0161 (596/37000). AF 95% confidence interval is 0.015. There are 5 homozygotes in gnomad4_exome. There are 289 alleles in male gnomad4_exome subpopulation. Median coverage is 18. This position pass quality control queck.
BS2
High Homozygotes in GnomAdExome4 at 5 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KIFC2 | NM_001369769.2 | c.*794G>A | 3_prime_UTR_variant | 18/18 | ENST00000645548.2 | NP_001356698.1 | ||
FOXH1 | NM_003923.3 | c.*55C>T | 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 | ENST00000645548.2 | c.*794G>A | 3_prime_UTR_variant | 18/18 | NM_001369769.2 | ENSP00000494595.1 | ||||
FOXH1 | ENST00000377317.5 | c.*55C>T | 3_prime_UTR_variant | 3/3 | 1 | NM_003923.3 | ENSP00000366534.4 | |||
KIFC2 | ENST00000643461.1 | n.3627G>A | non_coding_transcript_exon_variant | 17/17 |
Frequencies
GnomAD3 genomes AF: 0.000493 AC: 75AN: 152142Hom.: 1 Cov.: 32
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GnomAD4 exome AF: 0.000495 AC: 611AN: 1233936Hom.: 5 Cov.: 18 AF XY: 0.000476 AC XY: 289AN XY: 607284
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GnomAD4 genome AF: 0.000486 AC: 74AN: 152260Hom.: 1 Cov.: 32 AF XY: 0.000524 AC XY: 39AN XY: 74466
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Holoprosencephaly sequence Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at