chr4-55088977-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_002253.4(KDR):c.3405-4C>T variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000405 in 1,603,222 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (no stars).
Frequency
Consequence
NM_002253.4 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KDR | NM_002253.4 | c.3405-4C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000263923.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KDR | ENST00000263923.5 | c.3405-4C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_002253.4 | P1 | |||
ENST00000511222.1 | n.234-3336G>A | intron_variant, non_coding_transcript_variant | 5 | ||||||
KDR | ENST00000647068.1 | n.3418-4C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152194Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.0000434 AC: 63AN: 1451028Hom.: 0 Cov.: 28 AF XY: 0.0000429 AC XY: 31AN XY: 722712
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152194Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74350
ClinVar
Submissions by phenotype
Carcinoma of colon Uncertain:1
Uncertain significance, no assertion criteria provided | case-control | Immunobiology Lab; University of Kashmir | Jan 24, 2015 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at