chr3-41918514-T-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_017886.4(ULK4):c.670A>G(p.Ile224Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.803 in 1,581,668 control chromosomes in the GnomAD database, including 519,508 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 (★). 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.670A>G | p.Ile224Val | missense_variant | 7/37 | ENST00000301831.9 | |
ULK4 | NM_001322500.2 | c.670A>G | p.Ile224Val | missense_variant | 7/36 | ||
ULK4 | NM_001322501.2 | c.-161A>G | 5_prime_UTR_variant | 7/36 | |||
ULK4 | NR_136342.2 | n.806A>G | non_coding_transcript_exon_variant | 7/35 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ULK4 | ENST00000301831.9 | c.670A>G | p.Ile224Val | missense_variant | 7/37 | 2 | NM_017886.4 | P1 | |
ULK4 | ENST00000420927.5 | c.670A>G | p.Ile224Val | missense_variant | 7/18 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.680 AC: 102996AN: 151440Hom.: 38593 Cov.: 30
GnomAD3 exomes AF: 0.787 AC: 180629AN: 229482Hom.: 73091 AF XY: 0.793 AC XY: 98796AN XY: 124516
GnomAD4 exome AF: 0.816 AC: 1166405AN: 1430112Hom.: 480896 Cov.: 30 AF XY: 0.817 AC XY: 580337AN XY: 710256
GnomAD4 genome ? AF: 0.680 AC: 103031AN: 151556Hom.: 38612 Cov.: 30 AF XY: 0.681 AC XY: 50409AN XY: 73976
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