4-55106807-T-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_002253.4(KDR):c.1416A>T(p.Gln472His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.227 in 1,599,452 control chromosomes in the GnomAD database, including 44,436 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_002253.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KDR | NM_002253.4 | c.1416A>T | p.Gln472His | missense_variant | 11/30 | ENST00000263923.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KDR | ENST00000263923.5 | c.1416A>T | p.Gln472His | missense_variant | 11/30 | 1 | NM_002253.4 | P1 | |
KDR | ENST00000512566.1 | n.1416A>T | non_coding_transcript_exon_variant | 11/13 | 1 | ||||
KDR | ENST00000647068.1 | n.1429A>T | non_coding_transcript_exon_variant | 11/30 |
Frequencies
GnomAD3 genomes AF: 0.204 AC: 30976AN: 152078Hom.: 3610 Cov.: 33
GnomAD3 exomes AF: 0.223 AC: 55838AN: 250700Hom.: 7417 AF XY: 0.225 AC XY: 30538AN XY: 135550
GnomAD4 exome AF: 0.230 AC: 332586AN: 1447256Hom.: 40823 Cov.: 29 AF XY: 0.230 AC XY: 165501AN XY: 720958
GnomAD4 genome AF: 0.204 AC: 30991AN: 152196Hom.: 3613 Cov.: 33 AF XY: 0.207 AC XY: 15364AN XY: 74388
ClinVar
Submissions by phenotype
KDR-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Aug 02, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
not specified Other:1
not provided, no classification provided | reference population | ITMI | Sep 19, 2013 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at