rs58077086
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_017576.4(KIF27):āc.3439A>Gā(p.Met1147Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.224 in 1,611,616 control chromosomes in the GnomAD database, including 42,729 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ).
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.3439A>G | p.Met1147Val | missense_variant | 16/18 | ENST00000297814.7 | |
LOC124900638 | XR_007061620.1 | n.263+625T>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KIF27 | ENST00000297814.7 | c.3439A>G | p.Met1147Val | missense_variant | 16/18 | 1 | NM_017576.4 | P1 | |
ENST00000591217.5 | n.582+625T>C | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.175 AC: 26623AN: 152078Hom.: 2900 Cov.: 31
GnomAD3 exomes AF: 0.199 AC: 49852AN: 251066Hom.: 5449 AF XY: 0.202 AC XY: 27428AN XY: 135694
GnomAD4 exome AF: 0.229 AC: 334515AN: 1459420Hom.: 39823 Cov.: 31 AF XY: 0.228 AC XY: 165770AN XY: 726192
GnomAD4 genome ? AF: 0.175 AC: 26635AN: 152196Hom.: 2906 Cov.: 31 AF XY: 0.172 AC XY: 12781AN XY: 74396
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