9-83859200-T-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_017576.4(KIF27):āc.3106A>Gā(p.Asn1036Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.133 in 1,613,412 control chromosomes in the GnomAD database, including 14,901 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. N1036I) has been classified as Uncertain significance.
Frequency
Consequence
NM_017576.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KIF27 | NM_017576.4 | c.3106A>G | p.Asn1036Asp | missense_variant | 14/18 | ENST00000297814.7 | |
LOC124900638 | XR_007061620.1 | downstream_gene_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KIF27 | ENST00000297814.7 | c.3106A>G | p.Asn1036Asp | missense_variant | 14/18 | 1 | NM_017576.4 | P1 | |
ENST00000591217.5 | n.879+40T>C | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.134 AC: 20339AN: 152136Hom.: 1451 Cov.: 31
GnomAD3 exomes AF: 0.122 AC: 30733AN: 251410Hom.: 2038 AF XY: 0.122 AC XY: 16526AN XY: 135886
GnomAD4 exome AF: 0.133 AC: 194067AN: 1461158Hom.: 13443 Cov.: 32 AF XY: 0.131 AC XY: 95565AN XY: 726934
GnomAD4 genome AF: 0.134 AC: 20378AN: 152254Hom.: 1458 Cov.: 31 AF XY: 0.133 AC XY: 9935AN XY: 74452
ClinVar
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Mar 29, 2016 | Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at