rs775279070
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_002218.5(ITIH4):c.2426G>A(p.Ser809Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00017 in 1,613,928 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_002218.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ITIH4 | ENST00000266041.9 | c.2426G>A | p.Ser809Asn | missense_variant | Exon 21 of 24 | 1 | NM_002218.5 | ENSP00000266041.4 | ||
ENSG00000243696 | ENST00000468472.1 | n.*4062G>A | non_coding_transcript_exon_variant | Exon 21 of 24 | 2 | ENSP00000422253.1 | ||||
ENSG00000243696 | ENST00000468472.1 | n.*4062G>A | 3_prime_UTR_variant | Exon 21 of 24 | 2 | ENSP00000422253.1 |
Frequencies
GnomAD3 genomes AF: 0.000105 AC: 16AN: 152204Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000111 AC: 28AN: 251322Hom.: 0 AF XY: 0.000133 AC XY: 18AN XY: 135824
GnomAD4 exome AF: 0.000177 AC: 259AN: 1461724Hom.: 0 Cov.: 32 AF XY: 0.000187 AC XY: 136AN XY: 727176
GnomAD4 genome AF: 0.000105 AC: 16AN: 152204Hom.: 0 Cov.: 33 AF XY: 0.0000673 AC XY: 5AN XY: 74344
ClinVar
Submissions by phenotype
not specified 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