7-100803470-C-T
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_004444.5(EPHB4):c.2955G>A(p.Pro985Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000141 in 1,572,610 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_004444.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
EPHB4 | ENST00000358173.8 | c.2955G>A | p.Pro985Pro | synonymous_variant | Exon 17 of 17 | 1 | NM_004444.5 | ENSP00000350896.3 | ||
EPHB4 | ENST00000360620.7 | c.2799G>A | p.Pro933Pro | synonymous_variant | Exon 16 of 16 | 1 | ENSP00000353833.3 | |||
EPHB4 | ENST00000487222.5 | n.4156G>A | non_coding_transcript_exon_variant | Exon 16 of 16 | 1 | |||||
EPHB4 | ENST00000616502 | c.*1420G>A | 3_prime_UTR_variant | Exon 14 of 14 | 5 | ENSP00000482702.1 |
Frequencies
GnomAD3 genomes AF: 0.000276 AC: 42AN: 152168Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000350 AC: 70AN: 200208Hom.: 0 AF XY: 0.000336 AC XY: 36AN XY: 107176
GnomAD4 exome AF: 0.000127 AC: 180AN: 1420324Hom.: 0 Cov.: 30 AF XY: 0.000128 AC XY: 90AN XY: 700878
GnomAD4 genome AF: 0.000269 AC: 41AN: 152286Hom.: 0 Cov.: 32 AF XY: 0.000349 AC XY: 26AN XY: 74472
ClinVar
Submissions by phenotype
not provided Benign:1
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Cardiovascular phenotype Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at