rs4973986
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_017886.4(ULK4):āc.1918T>Gā(p.Ser640Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.844 in 1,613,390 control chromosomes in the GnomAD database, including 576,227 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.
Frequency
Consequence
NM_017886.4 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 |
---|---|---|---|---|---|---|---|
ULK4 | NM_017886.4 | c.1918T>G | p.Ser640Ala | missense_variant | 20/37 | ENST00000301831.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ULK4 | ENST00000301831.9 | c.1918T>G | p.Ser640Ala | missense_variant | 20/37 | 2 | NM_017886.4 | P1 | |
ULK4 | ENST00000460406.1 | n.399T>G | non_coding_transcript_exon_variant | 5/5 | 2 |
Frequencies
GnomAD3 genomes AF: 0.871 AC: 132422AN: 151980Hom.: 58112 Cov.: 31
GnomAD3 exomes AF: 0.851 AC: 211889AN: 249016Hom.: 90528 AF XY: 0.846 AC XY: 114362AN XY: 135110
GnomAD4 exome AF: 0.841 AC: 1229387AN: 1461292Hom.: 518048 Cov.: 45 AF XY: 0.841 AC XY: 611221AN XY: 726990
GnomAD4 genome AF: 0.871 AC: 132549AN: 152098Hom.: 58179 Cov.: 31 AF XY: 0.868 AC XY: 64517AN XY: 74334
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